diff --git a/.github/workflows/test_with_MFEM_master.yml b/.github/workflows/test_with_MFEM_master.yml index 4a9de9b2..4b49909e 100644 --- a/.github/workflows/test_with_MFEM_master.yml +++ b/.github/workflows/test_with_MFEM_master.yml @@ -18,22 +18,21 @@ jobs: matrix: python-version: ["3.7", "3.8", "3.9", "3.10"] #python-version: ["3.10"] - #os: [ubuntu-latest] os: [ubuntu-20.04] # USE_FLAGS : cuda, parallel, libceed env: - { USE_FLAGS: "000"} - - { USE_FLAGS: "100"} - - { USE_FLAGS: "010"} - - { USE_FLAGS: "110"} +# - { USE_FLAGS: "100"} +# - { USE_FLAGS: "010"} +# - { USE_FLAGS: "110"} include: - os: macos-latest python-version: 3.9 env: {USE_FLAGS: "000"} - - os: [ubuntu-20.04] - python-version: 3.9 - env: {USE_FLAGS: "001"} +# - os: [ubuntu-20.04] +# python-version: 3.9 +# env: {USE_FLAGS: "001"} # runs-on: ${{ matrix.os }} #env: ${{ matrix.env }} @@ -65,9 +64,10 @@ jobs: pip install six numpy --verbose if [ "${{matrix.python-version}}" = "3.10" ] ; then pip install numba numba-scipy --verbose - #pip install scipy + #pip install scipy numba --verbose else pip install numba numba-scipy --verbose + #pip install numba scipy --verbose fi if [ -f requirements.txt ]; then diff --git a/.gitignore b/.gitignore index 5ff6a178..0c6a51db 100644 --- a/.gitignore +++ b/.gitignore @@ -14,5 +14,7 @@ test/* !test/*.py !test/cpp !test/cpp/ +!test/issues/*.py +!test/issues/data_3960/VisIt_volume *.egg-info *.py# diff --git a/data/fichera-mixed.mesh b/data/fichera-mixed.mesh new file mode 100644 index 00000000..f98134f4 --- /dev/null +++ b/data/fichera-mixed.mesh @@ -0,0 +1,96 @@ +MFEM mesh v1.0 + +# +# MFEM Geometry Types (see mesh/geom.hpp): +# +# POINT = 0 +# SEGMENT = 1 +# TRIANGLE = 2 +# SQUARE = 3 +# TETRAHEDRON = 4 +# CUBE = 5 +# PRISM = 6 +# + +dimension +3 + +elements +14 +1 4 13 15 21 25 +1 4 12 13 15 21 +1 4 13 21 22 25 +1 4 15 24 21 25 +1 4 13 15 25 16 +1 5 0 1 4 3 9 10 13 12 +1 5 8 9 12 11 17 18 21 20 +1 5 2 3 6 5 11 12 15 14 +1 6 3 4 6 12 13 15 +1 6 4 7 6 13 16 15 +1 6 12 13 21 9 10 18 +1 6 13 22 21 10 19 18 +1 6 11 14 20 12 15 21 +1 6 15 21 24 14 20 23 + +boundary +30 + 1 3 5 6 3 2 + 2 2 3 6 4 + 2 2 4 6 7 + 3 3 3 4 1 0 + 4 3 11 12 9 8 + 5 3 2 3 12 11 + 6 3 0 1 10 9 + 7 2 9 10 18 + 7 2 10 19 18 + 8 3 8 9 18 17 + 9 3 1 4 13 10 +10 3 4 7 16 13 +11 2 13 16 25 +11 2 13 25 22 +12 3 10 13 22 19 +13 3 7 6 15 16 +14 3 6 5 14 15 +15 3 15 14 23 24 +16 2 16 15 25 +16 2 15 24 25 +17 3 5 2 11 14 +18 3 3 0 9 12 +19 3 11 8 17 20 +20 2 11 20 14 +20 2 14 20 23 +21 3 17 18 21 20 +22 3 18 19 22 21 +23 2 21 22 25 +23 2 21 25 24 +24 3 20 21 24 23 + +vertices +26 +3 +0 -1 -1 +1 -1 -1 +-1 0 -1 +0 0 -1 +1 0 -1 +-1 1 -1 +0 1 -1 +1 1 -1 +-1 -1 0 +0 -1 0 +1 -1 0 +-1 0 0 +0 0 0 +1 0 0 +-1 1 0 +0 1 0 +1 1 0 +-1 -1 1 +0 -1 1 +1 -1 1 +-1 0 1 +0 0 1 +1 0 1 +-1 1 1 +0 1 1 +1 1 1 diff --git a/examples/ex18.py b/examples/ex18.py index 5c8eb569..772f8e96 100644 --- a/examples/ex18.py +++ b/examples/ex18.py @@ -171,7 +171,7 @@ def run(problem=1, # 10. Compute the L2 solution error summed for all components. if (t_final == 2.0): error = sol.ComputeLpError(2., u0) - print("Solution error: " + str(error)) + print("Solution error: " + "{:g}".format(error)) if __name__ == "__main__": diff --git a/examples/ex18_common.py b/examples/ex18_common.py index e23a06c2..9664f718 100644 --- a/examples/ex18_common.py +++ b/examples/ex18_common.py @@ -116,7 +116,7 @@ def Mult(self, x, y): y.SetSubVector(vdofs, ymat.GetData()) -class DomainIntegrator(mfem.BilinearFormIntegrator): +class DomainIntegrator(mfem.PyBilinearFormIntegrator): def __init__(self, dim): num_equation = globals()['num_equation'] self.flux = mfem.DenseMatrix(num_equation, dim) @@ -165,7 +165,7 @@ def AssembleElementMatrix2(self, trial_fe, test_fe, Tr, elmat): self.dshapedx[j, d] -class FaceIntegrator(mfem.NonlinearFormIntegrator): +class FaceIntegrator(mfem.PyNonlinearFormIntegrator): def __init__(self, rsolver, dim): self.rsolver = rsolver self.shape1 = mfem.Vector() diff --git a/examples/ex23.py b/examples/ex23.py index 820c253f..e1d8fcb8 100644 --- a/examples/ex23.py +++ b/examples/ex23.py @@ -199,7 +199,7 @@ def EvalValue(self, x): visualization = False print("GLVis visualization disabled.") else: - sout.precision(precision) + sout.precision(output.precision) sout << "solution\n" << mesh << dudt_gf sout << "pause\n" sout.flush() diff --git a/examples/ex33p.py b/examples/ex33p.py index 51f371a6..de4bb43e 100644 --- a/examples/ex33p.py +++ b/examples/ex33p.py @@ -1,5 +1,5 @@ ''' - MFEM example 33 + MFEM example 33p See c++ version in the MFEM library for more detail diff --git a/examples/ex34.py b/examples/ex34.py new file mode 100644 index 00000000..25dd1819 --- /dev/null +++ b/examples/ex34.py @@ -0,0 +1,476 @@ +''' + PyMFEM example 34 + + See c++ version in the MFEM library for more detail + + Sample runs: python ex34.py -o 2 + python ex34.py -pa -hex + + Device sample runs: + python ex34.py -o 2 -pa -hex -d cuda + python ex34.py -o 2 -no-pa -d cuda + +''' +import mfem.ser as mfem +from mfem.ser import intArray, doubleArray +import os +from os.path import expanduser, join +import numpy as np +from numpy import sin, cos, array, pi, sqrt, floor + +pa = False +algebraic_ceed = False +visualization = True + + +def run(ref_levels=1, + order=1, + delta_const=1e-6, + static_cond=False, + mixed=True, + device_config="cpu", + use_umfpack=False): + + cond_attr = mfem.intArray() + + mesh_file = "../data/fichera-mixed.mesh" + if not mixed or pa: + mesh_file = "../data/fichera.mesh" + + if mesh_file == "../data/fichera-mixed.mesh": + submesh_elems = mfem.intArray([0, 2, 3, 4, 9]) + else: + submesh_elems = mfem.intArray([10, 14, 34, 36, 37, 38, 39]) + + sym_plane_attr = mfem.intArray([9, 10, 11, 12, 13, 14, 15, 16, ]) + + phi0_attr = mfem.intArray() + phi1_attr = mfem.intArray() + jn_zero_attr = mfem.intArray() + + if (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh"): + phi0_attr.Append(2) + + if (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh"): + phi1_attr.Append(23) + + if (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh"): + jn_zero_attr.Append(25) + for i in range(sym_plane_attr.Size()): + jn_zero_attr.Append(sym_plane_attr[i]) + + # 2. Enable hardware devices such as GPUs, and programming models such as + # CUDA, OCCA, RAJA and OpenMP based on command line options. + device = mfem.Device(device_config) + device.Print() + + # 3. Read the (serial) mesh from the given mesh file on all processors. We + # can handle triangular, quadrilateral, tetrahedral, hexahedral, surface + # and volume meshes with the same code. + mesh_file = expanduser( + join(os.path.dirname(__file__), *mesh_file.split("/"))) + mesh = mfem.Mesh(mesh_file, 1, 1) + dim = mesh.Dimension() + if not mixed or pa: + mesh.UniformRefinement() + if ref_levels > 0: + ref_levels = ref_levels - 1 + submesh_attr = -1 + + if cond_attr.Size() == 0 and submesh_elems.Size() > 0: + max_attr = mesh.attributes.Max() + submesh_attr = max_attr + 1 + + for i in range(submesh_elems.Size()): + mesh.SetAttribute(submesh_elems[i], submesh_attr) + mesh.SetAttributes() + if cond_attr.Size() == 0: + cond_attr.Append(submesh_attr) + + # 4. Refine the serial mesh on all processors to increase the resolution. In + # this example we do 'ref_levels' of uniform refinement. + for l in range(ref_levels): + mesh.UniformRefinement() + + # 5b. Extract a submesh covering a portion of the domain + mesh_cond = mfem.SubMesh.CreateFromDomain(mesh, cond_attr) + + # 6. Define a suitable finite element space on the SubMesh and compute + # the current density as an H(div) field. + fec_cond_rt = mfem.RT_FECollection(order - 1, dim) + fes_cond_rt = mfem.FiniteElementSpace(mesh_cond, fec_cond_rt) + j_cond = mfem.GridFunction(fes_cond_rt) + + ComputeCurrentDensityOnSubMesh(order, phi0_attr, phi1_attr, jn_zero_attr, + j_cond, use_umfpack) + + # 6a. Save the SubMesh and associated current density in parallel. This + # output can be viewed later using GLVis: + # "glvis -np -m cond_mesh -g cond_j" + mesh_cond.Print("cond.mesh", 8) + j_cond.Save("cond_j.gf", 8) + + # 6b. Send the current density, computed on the SubMesh, to a GLVis server. + if visualization: + port_sock = mfem.socketstream("localhost", 19916) + port_sock.precision(8) + port_sock << "solution\n" << mesh_cond << j_cond + port_sock << "window_title 'Conductor J'" + port_sock << "window_geometry 400 0 400 350" + port_sock.flush() + + # 7. Define a parallel finite element space on the full mesh. Here we use + # the H(curl) finite elements for the vector potential and H(div) for the + # current density. + fec_nd = mfem.ND_FECollection(order, dim) + fec_rt = mfem.RT_FECollection(order - 1, dim) + fespace_nd = mfem.FiniteElementSpace(mesh, fec_nd) + fespace_rt = mfem.FiniteElementSpace(mesh, fec_rt) + + j_full = mfem.GridFunction(fespace_rt) + j_full.Assign(0.0) + mesh_cond.Transfer(j_cond, j_full) + + # 7a. Send the transferred current density to a GLVis server. + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock.precision(8) + sol_sock << "solution\n" << mesh << j_full + sol_sock << "window_title 'J Full'" + sol_sock << "window_geometry 400 430 400 350" + sol_sock.flush() + + # 8. Determine the list of true (i.e. parallel conforming) essential + # boundary dofs. In this example, the boundary conditions are defined by + # marking all the boundary attributes except for those on a symmetry + # plane as essential (Dirichlet) and converting them to a list of true + # dofs. + ess_tdof_list = mfem.intArray() + ess_bdr = mfem.intArray() + if mesh.bdr_attributes.Size(): + ess_bdr.SetSize(mesh.bdr_attributes.Max()) + ess_bdr.Assign(1) + for i in range(sym_plane_attr.Size()): + ess_bdr[sym_plane_attr[i]-1] = 0 + fespace_nd.GetEssentialTrueDofs(ess_bdr, ess_tdof_list) + + # 9. Set up the parallel linear form b(.) which corresponds to the + # right-hand side of the FEM linear system, which in this case is + # (J,W_i) where J is given by the function H(div) field transferred + # from the SubMesh and W_i are the basis functions in the finite + # element fespace. + jCoef = mfem.VectorGridFunctionCoefficient(j_full) + b = mfem.LinearForm(fespace_nd) + b.AddDomainIntegrator(mfem.VectorFEDomainLFIntegrator(jCoef)) + b.Assemble() + + # 10. Define the solution vector x as a parallel finite element grid + # function corresponding to fespace. Initialize x to zero. + x = mfem.GridFunction(fespace_nd) + x.Assign(0.0) + + # 11. Set up the parallel bilinear form corresponding to the EM diffusion + # operator curl muinv curl + delta I, by adding the curl-curl and the + # mass domain integrators. For standard magnetostatics equations choose + # delta << 1. Larger values of delta should make the linear system + # easier to solve at the expense of resembling a diffusive quasistatic + # magnetic field. A reasonable balance must be found whenever the mesh + # or problem setup is altered. + muinv = mfem.ConstantCoefficient(1.0) + delta = mfem.ConstantCoefficient(delta_const) + a = mfem.BilinearForm(fespace_nd) + if pa: + a.SetAssemblyLevel(mfem.AssemblyLevel_PARTIAL) + a.AddDomainIntegrator(mfem.CurlCurlIntegrator(muinv)) + a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(delta)) + + # 12. Assemble the parallel bilinear form and the corresponding linear + # system, applying any necessary transformations such as: parallel + # assembly, eliminating boundary conditions, applying conforming + # constraints for non-conforming AMR, static condensation, etc. + if static_cond: + a.EnableStaticCondensation() + a.Assemble() + + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + a.FormLinearSystem(ess_tdof_list, x, b, A, X, B) + + # 13. Solve the system AX=B + if pa: # Jacobi preconditioning in partial assembly mode + print("\n".join(("\nSolving for magnetic vector potential ", + "using CG with a Jacobi preconditioner"))) + + M = mfem.OperatorJacobiSmoother(a, ess_tdof_list) + mfem.PCG(A, M, B, X, 1, 1000, 1e-12, 0.0) + + else: + if not use_umfpack: + print("\n".join(("\nSolving for magnetic vector potential ", + "using CG with a Gauss-Seidel preconditioner"))) + + # 13a. Define a simple symmetric Gauss-Seidel preconditioner and use + # it to solve the system Ax=b with PCG. + AA = mfem.OperatorHandle2SparseMatrix(A) + M = mfem.GSSmoother(AA) + mfem.PCG(A, M, B, X, 1, 500, 1e-12, 0.0) + + else: + print("".join(("\nSolving for magnetic vector potential ", + "using UMFPack"))) + + # 13a. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the + # system. + umf_solver = mfem.UMFPackSolver() + umf_solver.Control[ + mfem.UMFPACK_ORDERING] = mfem.UMFPACK_ORDERING_METIS + umf_solver.SetOperator(A) + umf_solver.Mult(B, X) + + # 14. Recover the parallel grid function corresponding to X. This is the + # local finite element solution on each processor. + a.RecoverFEMSolution(X, b, x) + + # 15. Save the refined mesh and the solution in parallel. This output can + # be viewed later using GLVis: "glvis -m refined.mesh -g sol.gf". + mesh.Print("refined.mesh", 8) + x.Save("sol.gf", 8) + + # 16. Send the solution by socket to a GLVis server. + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock << "solution\n" << mesh << x + sol_sock << "window_title 'Vector Potential'" + sol_sock << "window_geometry 800 0 400 350" + sol_sock.flush() + + # 17. Compute the magnetic flux as the curl of the solution + curl = mfem.DiscreteLinearOperator(fespace_nd, fespace_rt) + curl.AddDomainInterpolator(mfem.CurlInterpolator()) + curl.Assemble() + curl.Finalize() + + dx = mfem.GridFunction(fespace_rt) + curl.Mult(x, dx) + + # 18. Save the curl of the solution in parallel. This output can be viewed + # later using GLVis: "glvis -m refined.mesh -g dsol.gf". + dx.Save("dsol.gf", 8) + + # 19. Send the curl of the solution by socket to a GLVis server. + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock.precision(8) + sol_sock << "solution\n" << mesh << dx + sol_sock << "window_title 'Magnetic Flux'" + sol_sock << "window_geometry 1200 0 400 350" + sol_sock.flush() + + +def ComputeCurrentDensityOnSubMesh(order, phi0_attr, phi1_attr, jn_zero_attr, + j_cond, use_umfpack): + # Extract the finite element space and mesh on which j_cond is defined + fes_cond_rt = j_cond.FESpace() + mesh_cond = fes_cond_rt.GetMesh() + dim = mesh_cond.Dimension() + + # Define a parallel finite element space on the SubMesh. Here we use the H1 + # finite elements for the electrostatic potential. + fec_h1 = mfem.H1_FECollection(order, dim) + fes_cond_h1 = mfem.FiniteElementSpace(mesh_cond, fec_h1) + + # Define the conductivity coefficient and the boundaries associated with the + # fixed potentials phi0 and phi1 which will drive the current. + sigmaCoef = mfem.ConstantCoefficient(1.0) + ess_bdr_phi = mfem.intArray(mesh_cond.bdr_attributes.Max()) + ess_bdr_j = mfem.intArray(mesh_cond.bdr_attributes.Max()) + ess_bdr_tdof_phi = mfem.intArray() + ess_bdr_phi.Assign(0) + ess_bdr_j.Assign(0) + + for i in range(phi0_attr.Size()): + ess_bdr_phi[phi0_attr[i]-1] = 1 + + for i in range(phi1_attr.Size()): + ess_bdr_phi[phi1_attr[i]-1] = 1 + + for i in range(jn_zero_attr.Size()): + ess_bdr_j[jn_zero_attr[i]-1] = 1 + + fes_cond_h1.GetEssentialTrueDofs(ess_bdr_phi, ess_bdr_tdof_phi) + + # Setup the bilinear form corresponding to -Div(sigma Grad phi) + a_h1 = mfem.BilinearForm(fes_cond_h1) + a_h1.AddDomainIntegrator(mfem.DiffusionIntegrator(sigmaCoef)) + a_h1.Assemble() + + # Set the r.h.s. to zero + b_h1 = mfem.LinearForm(fes_cond_h1) + b_h1.Assign(0.0) + + # Setup the boundary conditions on phi + one = mfem.ConstantCoefficient(1.0) + zero = mfem.ConstantCoefficient(0.0) + phi_h1 = mfem.GridFunction(fes_cond_h1) + phi_h1.Assign(0.0) + + bdr0 = mfem.intArray([0]*mesh_cond.bdr_attributes.Max()) + for i in range(phi0_attr.Size()): + bdr0[phi0_attr[i]-1] = 1 + + phi_h1.ProjectBdrCoefficient(zero, bdr0) + + bdr1 = mfem.intArray([0]*mesh_cond.bdr_attributes.Max()) + for i in range(phi1_attr.Size()): + bdr1[phi1_attr[i]-1] = 1 + + phi_h1.ProjectBdrCoefficient(one, bdr1) + + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + a_h1.FormLinearSystem(ess_bdr_tdof_phi, phi_h1, b_h1, A, X, B) + + # Solve the linear system + + if not pa: + if not use_umfpack: + print("".join(("\nSolving for electric potential using PCG ", + "with a Gauss-Seidel preconditioner"))) + + # Use a simple symmetric Gauss-Seidel preconditioner with PCG. + AA = mfem.OperatorHandle2SparseMatrix(A) + M = mfem.GSSmoother(AA) + mfem.PCG(AA, M, B, X, 1, 200, 1e-12, 0.0) + else: + print("\nSolving for electric potential using UMFPack") + + # If MFEM was compiled with SuiteSparse, + # use UMFPACK to solve the system. + umf_solver = mfem.UMFPackSolver() + umf_solver.Control[mfem.UMFPACK_ORDERING] = mfem.UMFPACK_ORDERING_METIS + umf_solver.SetOperator(A) + umf_solver.Mult(B, X) + else: + print("\nSolving for electric potential using CG") + + if mfem.UsesTensorBasis(fes_cond_h1): + if algebraic_ceed: + assert False, "not supported" + # prec = new ceed::AlgebraicSolver(a, ess_tdof_list); + # PCG(*A, M, B, X, 1, 400, 1e-12, 0.0); + else: + M = mfem.OperatorJacobiSmoother(a_h1, ess_bdr_tdof_phi) + mfem.PCG(A, M, B, X, 1, 400, 1e-12, 0.0) + else: + mfem.CG(A, B, X, 1, 400, 1e-12, 0.0) + a_h1.RecoverFEMSolution(X, b_h1, phi_h1) + + # visualization + if visualization: + port_sock = mfem.socketstream("localhost", 19916) + port_sock.precision(8) + port_sock << "solution\n" << mesh_cond << phi_h1 + port_sock << "window_title 'Conductor Potential'" + port_sock << "window_geometry 0 0 400 350" + port_sock.flush() + + # Solve for the current density J = -sigma Grad phi with boundary conditions + # J.n = 0 on the walls of the conductor but not on the ports where phi=0 and + # phi=1. + + # J will be computed in H(div) so we need an RT mass matrix + m_rt = mfem.BilinearForm(fes_cond_rt) + m_rt.AddDomainIntegrator(mfem.VectorFEMassIntegrator()) + m_rt.Assemble() + + # Assemble the (sigma Grad phi) operator + d_h1 = mfem.MixedBilinearForm(fes_cond_h1, fes_cond_rt) + d_h1.AddDomainIntegrator(mfem.MixedVectorGradientIntegrator(sigmaCoef)) + d_h1.Assemble() + + # Compute the r.h.s, b_rt = sigma E = -sigma Grad phi + b_rt = mfem.LinearForm(fes_cond_rt) + d_h1.Mult(phi_h1, b_rt) + b_rt *= -1.0 + + # Apply the necessary boundary conditions and solve for J in H(div) + print("\nSolving for current density in H(Div), using diagonally scaled CG") + print("Size of linear system: " + str(fes_cond_rt.GetTrueVSize())) + + ess_bdr_tdof_rt = mfem.intArray() + M = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + + fes_cond_rt.GetEssentialTrueDofs(ess_bdr_j, ess_bdr_tdof_rt) + j_cond.Assign(0.0) + m_rt.FormLinearSystem(ess_bdr_tdof_rt, j_cond, b_rt, M, X, B) + + cg = mfem.CGSolver() + cg.SetRelTol(1e-12) + cg.SetMaxIter(2000) + cg.SetPrintLevel(1) + cg.SetOperator(M) + cg.Mult(B, X) + m_rt.RecoverFEMSolution(X, b_rt, j_cond) + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser( + description='Ex34 (Sourse Function using a Submehs Transfer )') + + parser.add_argument('-r', '--refine', + action='store', default=1, type=int, + help="Number of times to refine the mesh uniformly.") + parser.add_argument("-o", "--order", + action='store', default=1, type=int, + help="Finite element order (polynomial degree).") + parser.add_argument("-mc", "--magnetic-cond", + action='store', default=1e-6, type=float, + help="Magnetic Conductivity") + parser.add_argument("-sc", "--static-condensation", + action='store_true', + help="Enable static condensation.") + parser.add_argument("-hex", "--hex-mesh", + action='store_true', default=False, + help="Mixed mesh of hexahedral mesh.") + parser.add_argument("-pa", "--partial-assembly", + action='store_true', + help="Enable Partial Assembly.") + parser.add_argument("-d", "--device", + default="cpu", type=str, + help="Device configuration string, see Device::Configure().") + parser.add_argument("-no-vis", "--no-visualization", + action='store_false', default=True, + help='Enable GLVis visualization') + + if hasattr(mfem, "UMFPackSolver"): + parser.add_argument("-noumfpack", "--no-use-umfpack", + action='store_true', default=False, + help='Enable UMFPACK') + + args = parser.parse_args() + parser.print_options(args) + + globals()["pa"] = args.partial_assembly + globals()["visualization"] = args.no_visualization + + if hasattr(mfem, "UMFPackSolver"): + use_umfpack = True if not args.no_use_umfpack else False + else: + use_umfpack = False + + run(ref_levels=args.refine, + order=args.order, + delta_const=args.magnetic_cond, + static_cond=args.static_condensation, + mixed=(not args.hex_mesh), + device_config=args.device, + use_umfpack=use_umfpack) diff --git a/examples/ex34p.py b/examples/ex34p.py new file mode 100644 index 00000000..cbe00cee --- /dev/null +++ b/examples/ex34p.py @@ -0,0 +1,476 @@ +''' + PyMFEM example 34p + + See c++ version in the MFEM library for more detail + + Sample runs: mpirun -np 4 python ex34p.py -o 2 + mpirun -np 4 python ex34p.py -pa -hex + + Device sample runs: + mpirun -np 4 python ex34p.py -o 2 -pa -hex -d cuda + mpirun -np 4 python ex34p.py -o 2 -no-pa -d cuda + +''' +import mfem.par as mfem +from mfem.par import intArray, doubleArray +import os +from os.path import expanduser, join +import numpy as np +from numpy import sin, cos, array, pi, sqrt, floor + +from mpi4py import MPI +num_procs = MPI.COMM_WORLD.size +myid = MPI.COMM_WORLD.rank +smyid = '.{:0>6d}'.format(myid) + +pa = False +algebraic_ceed = False +visualization = True + +def run(ser_ref_levels=1, + par_ref_levels=1, + order=1, + delta_const=1e-6, + static_cond=False, + mixed=True, + device_config="cpu"): + + cond_attr = mfem.intArray() + + mesh_file = "../data/fichera-mixed.mesh" + if not mixed or pa: + mesh_file = "../data/fichera.mesh" + + if mesh_file == "../data/fichera-mixed.mesh": + submesh_elems = mfem.intArray([0, 2, 3, 4, 9]) + else: + submesh_elems = mfem.intArray([10, 14, 34, 36, 37, 38, 39]) + + sym_plane_attr = mfem.intArray([9, 10, 11, 12, 13, 14, 15, 16, ]) + + phi0_attr = mfem.intArray() + phi1_attr = mfem.intArray() + jn_zero_attr = mfem.intArray() + + if (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh"): + phi0_attr.Append(2) + + if (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh"): + phi1_attr.Append(23) + + if (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh"): + jn_zero_attr.Append(25) + for i in range(sym_plane_attr.Size()): + jn_zero_attr.Append(sym_plane_attr[i]) + + # 3. Enable hardware devices such as GPUs, and programming models such as + # CUDA, OCCA, RAJA and OpenMP based on command line options. + device = mfem.Device(device_config) + device.Print() + + # 4. Read the (serial) mesh from the given mesh file on all processors. We + # can handle triangular, quadrilateral, tetrahedral, hexahedral, surface + # and volume meshes with the same code. + mesh_file = expanduser( + join(os.path.dirname(__file__), *mesh_file.split("/"))) + mesh = mfem.Mesh(mesh_file, 1, 1) + dim = mesh.Dimension() + if not mixed or pa: + mesh.UniformRefinement() + if ser_ref_levels > 0: + ser_ref_levels = ser_ref_levels - 1 + else: + par_ref_levels = par_ref_levels - 1 + submesh_attr = -1 + + if cond_attr.Size() == 0 and submesh_elems.Size() > 0: + max_attr = mesh.attributes.Max() + submesh_attr = max_attr + 1 + + for i in range(submesh_elems.Size()): + mesh.SetAttribute(submesh_elems[i], submesh_attr) + mesh.SetAttributes() + if cond_attr.Size() == 0: + cond_attr.Append(submesh_attr) + + # 5. Refine the serial mesh on all processors to increase the resolution. In + # this example we do 'ref_levels' of uniform refinement. + + for l in range(ser_ref_levels): + mesh.UniformRefinement() + + # 6. Define a parallel mesh by a partitioning of the serial mesh. Refine + # this mesh further in parallel to increase the resolution. Once the + # parallel mesh is defined, the serial mesh can be deleted. + pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) + del mesh + for l in range(par_ref_levels): + pmesh.UniformRefinement() + + # 6b. Extract a submesh covering a portion of the domain + pmesh_cond = mfem.ParSubMesh.CreateFromDomain(pmesh, cond_attr) + + # 7. Define a suitable finite element space on the SubMesh and compute + # the current density as an H(div) field. + fec_cond_rt = mfem.RT_FECollection(order - 1, dim) + fes_cond_rt = mfem.ParFiniteElementSpace(pmesh_cond, fec_cond_rt) + j_cond = mfem.ParGridFunction(fes_cond_rt) + + ComputeCurrentDensityOnSubMesh( + order, phi0_attr, phi1_attr, jn_zero_attr, j_cond) + + # 7a. Save the SubMesh and associated current density in parallel. This + # output can be viewed later using GLVis: + # "glvis -np -m cond_mesh -g cond_j" + pmesh_cond.Print("cond_mesh"+smyid, 8) + j_cond.Save("cond_j"+smyid, 8) + + # 7b. Send the current density, computed on the SubMesh, to a GLVis server. + if visualization: + port_sock = mfem.socketstream("localhost", 19916) + port_sock << "parallel " << num_procs << " " << myid << "\n" + port_sock.precision(8) + port_sock << "solution\n" << pmesh_cond << j_cond + port_sock << "window_title 'Conductor J'" + port_sock << "window_geometry 400 0 400 350" + port_sock.flush() + + # 8. Define a parallel finite element space on the full mesh. Here we use + # the H(curl) finite elements for the vector potential and H(div) for the + # current density. + fec_nd = mfem.ND_FECollection(order, dim) + fec_rt = mfem.RT_FECollection(order - 1, dim) + fespace_nd = mfem.ParFiniteElementSpace(pmesh, fec_nd) + fespace_rt = mfem.ParFiniteElementSpace(pmesh, fec_rt) + + j_full = mfem.ParGridFunction(fespace_rt) + j_full.Assign(0.0) + pmesh_cond.Transfer(j_cond, j_full) + + # 8a. Send the transferred current density to a GLVis server. + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock << "parallel " << num_procs << " " << myid << "\n" + sol_sock.precision(8) + sol_sock << "solution\n" << pmesh << j_full + sol_sock << "window_title 'J Full'" + sol_sock << "window_geometry 400 430 400 350" + sol_sock.flush() + + # 9. Determine the list of true (i.e. parallel conforming) essential + # boundary dofs. In this example, the boundary conditions are defined by + # marking all the boundary attributes except for those on a symmetry + # plane as essential (Dirichlet) and converting them to a list of true + # dofs. + ess_tdof_list = mfem.intArray() + ess_bdr = mfem.intArray() + if pmesh.bdr_attributes.Size(): + ess_bdr.SetSize(pmesh.bdr_attributes.Max()) + ess_bdr.Assign(1) + for i in range(sym_plane_attr.Size()): + ess_bdr[sym_plane_attr[i]-1] = 0 + fespace_nd.GetEssentialTrueDofs(ess_bdr, ess_tdof_list) + + # 10. Set up the parallel linear form b(.) which corresponds to the + # right-hand side of the FEM linear system, which in this case is + # (J,W_i) where J is given by the function H(div) field transferred + # from the SubMesh and W_i are the basis functions in the finite + # element fespace. + jCoef = mfem.VectorGridFunctionCoefficient(j_full) + b = mfem.ParLinearForm(fespace_nd) + b.AddDomainIntegrator(mfem.VectorFEDomainLFIntegrator(jCoef)) + b.Assemble() + + # 11. Define the solution vector x as a parallel finite element grid + # function corresponding to fespace. Initialize x to zero. + x = mfem.ParGridFunction(fespace_nd) + x.Assign(0.0) + + # 12. Set up the parallel bilinear form corresponding to the EM diffusion + # operator curl muinv curl + delta I, by adding the curl-curl and the + # mass domain integrators. For standard magnetostatics equations choose + # delta << 1. Larger values of delta should make the linear system + # easier to solve at the expense of resembling a diffusive quasistatic + # magnetic field. A reasonable balance must be found whenever the mesh + # or problem setup is altered. + muinv = mfem.ConstantCoefficient(1.0) + delta = mfem.ConstantCoefficient(delta_const) + a = mfem.ParBilinearForm(fespace_nd) + if pa: + a.SetAssemblyLevel(mfem.AssemblyLevel_PARTIAL) + a.AddDomainIntegrator(mfem.CurlCurlIntegrator(muinv)) + a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(delta)) + + # 13. Assemble the parallel bilinear form and the corresponding linear + # system, applying any necessary transformations such as: parallel + # assembly, eliminating boundary conditions, applying conforming + # constraints for non-conforming AMR, static condensation, etc. + if static_cond: + a.EnableStaticCondensation() + a.Assemble() + + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + a.FormLinearSystem(ess_tdof_list, x, b, A, X, B) + + # 14. Solve the system AX=B using PCG with an AMS preconditioner. + if myid == 0: + print("\n".join(("\nSolving for magnetic vector potential ", + "using CG with AMS"))) + + if pa: # Jacobi preconditioning in partial assembly mode + ams = mfem.MatrixFreeAMS(a, A, fespace_nd, muinv, delta, None, ess_bdr) + cg = mfem.CGSolver(MPI.COMM_WORLD) + cg.SetRelTol(1e-12) + cg.SetMaxIter(1000) + cg.SetPrintLevel(1) + cg.SetOperator(*A) + cg.SetPreconditioner(ams) + cg.Mult(B, X) + + else: + AM = A.AsHypreParMatrix() + if myid == 0: + print("\nSize of linear system: "+str(AM.GetGlobalNumRows())) + + prec_fespace = a.SCParFESpace() if a.StaticCondensationIsEnabled() else fespace_nd + + ams = mfem.HypreAMS(AM, prec_fespace) + pcg = mfem.HyprePCG(AM) + pcg.SetTol(1e-12) + pcg.SetMaxIter(500) + pcg.SetPrintLevel(2) + pcg.SetPreconditioner(ams) + pcg.Mult(B, X) + + # 15. Recover the parallel grid function corresponding to X. This is the + # local finite element solution on each processor. + a.RecoverFEMSolution(X, b, x) + + # 16. Save the refined mesh and the solution in parallel. This output can + # be viewed later using GLVis: "glvis -np -m mesh -g sol". + pmesh.Print("mesh"+smyid, 8) + x.Save("sol"+smyid, 8) + + # 17. Send the solution by socket to a GLVis server. + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock << "parallel " << num_procs << " " << myid << "\n" + sol_sock << "solution\n" << pmesh << x + sol_sock << "window_title 'Vector Potential'" + sol_sock << "window_geometry 800 0 400 350" + sol_sock.flush() + + # 18. Compute the magnetic flux as the curl of the solution + curl = mfem.ParDiscreteLinearOperator(fespace_nd, fespace_rt) + curl.AddDomainInterpolator(mfem.CurlInterpolator()) + curl.Assemble() + curl.Finalize() + + dx = mfem.ParGridFunction(fespace_rt) + curl.Mult(x, dx) + + # 19. Save the curl of the solution in parallel. This output can be viewed + # later using GLVis: "glvis -np -m mesh -g dsol". + dx.Save("dsol"+smyid, 8) + + # 19. Send the curl of the solution by socket to a GLVis server. + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock << "parallel " << num_procs << " " << myid << "\n" + sol_sock.precision(8) + sol_sock << "solution\n" << pmesh << dx + sol_sock << "window_title 'Magnetic Flux'" + sol_sock << "window_geometry 1200 0 400 350" + sol_sock.flush() + + +def ComputeCurrentDensityOnSubMesh(order, phi0_attr, phi1_attr, jn_zero_attr, + j_cond): + # Extract the finite element space and mesh on which j_cond is defined + fes_cond_rt = j_cond.ParFESpace() + pmesh_cond = fes_cond_rt.GetParMesh() + dim = pmesh_cond.Dimension() + + # Define a parallel finite element space on the SubMesh. Here we use the H1 + # finite elements for the electrostatic potential. + fec_h1 = mfem.H1_FECollection(order, dim) + fes_cond_h1 = mfem.ParFiniteElementSpace(pmesh_cond, fec_h1) + + # Define the conductivity coefficient and the boundaries associated with the + # fixed potentials phi0 and phi1 which will drive the current. + sigmaCoef = mfem.ConstantCoefficient(1.0) + ess_bdr_phi = mfem.intArray(pmesh_cond.bdr_attributes.Max()) + ess_bdr_j = mfem.intArray(pmesh_cond.bdr_attributes.Max()) + ess_bdr_tdof_phi = mfem.intArray() + ess_bdr_phi.Assign(0) + ess_bdr_j.Assign(0) + + for i in range(phi0_attr.Size()): + ess_bdr_phi[phi0_attr[i]-1] = 1 + + for i in range(phi1_attr.Size()): + ess_bdr_phi[phi1_attr[i]-1] = 1 + + for i in range(jn_zero_attr.Size()): + ess_bdr_j[jn_zero_attr[i]-1] = 1 + + fes_cond_h1.GetEssentialTrueDofs(ess_bdr_phi, ess_bdr_tdof_phi) + + # Setup the bilinear form corresponding to -Div(sigma Grad phi) + a_h1 = mfem.ParBilinearForm(fes_cond_h1) + a_h1.AddDomainIntegrator(mfem.DiffusionIntegrator(sigmaCoef)) + a_h1.Assemble() + + # Set the r.h.s. to zero + b_h1 = mfem.ParLinearForm(fes_cond_h1) + b_h1.Assign(0.0) + + # Setup the boundary conditions on phi + one = mfem.ConstantCoefficient(1.0) + zero = mfem.ConstantCoefficient(0.0) + phi_h1 = mfem.GridFunction(fes_cond_h1) + phi_h1.Assign(0.0) + + bdr0 = mfem.intArray([0]*pmesh_cond.bdr_attributes.Max()) + for i in range(phi0_attr.Size()): + bdr0[phi0_attr[i]-1] = 1 + + phi_h1.ProjectBdrCoefficient(zero, bdr0) + + bdr1 = mfem.intArray([0]*pmesh_cond.bdr_attributes.Max()) + for i in range(phi1_attr.Size()): + bdr1[phi1_attr[i]-1] = 1 + + phi_h1.ProjectBdrCoefficient(one, bdr1) + + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + a_h1.FormLinearSystem(ess_bdr_tdof_phi, phi_h1, b_h1, A, X, B) + + # Solve the linear system using algebraic multigrid + if myid == 0: + print("\nSolving for electric potential using CG with AMG") + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + a_h1.FormLinearSystem(ess_bdr_tdof_phi, phi_h1, b_h1, A, X, B) + + prec = mfem.HypreBoomerAMG() + cg = mfem.CGSolver(MPI.COMM_WORLD) + cg.SetRelTol(1e-12) + cg.SetMaxIter(2000) + cg.SetPrintLevel(1) + cg.SetPreconditioner(prec) + cg.SetOperator(A.Ptr()) + cg.Mult(B, X) + a_h1.RecoverFEMSolution(X, b_h1, phi_h1) + + # visualization + if visualization: + port_sock = mfem.socketstream("localhost", 19916) + port_sock << "parallel " << num_procs << " " << myid << "\n" + port_sock.precision(8) + port_sock << "solution\n" << pmesh_cond << phi_h1 + port_sock << "window_title 'Conductor Potential'" + port_sock << "window_geometry 0 0 400 350" + port_sock.flush() + + # Solve for the current density J = -sigma Grad phi with boundary conditions + # J.n = 0 on the walls of the conductor but not on the ports where phi=0 and + # phi=1. + + # J will be computed in H(div) so we need an RT mass matrix + m_rt = mfem.ParBilinearForm(fes_cond_rt) + m_rt.AddDomainIntegrator(mfem.VectorFEMassIntegrator()) + m_rt.Assemble() + + # Assemble the (sigma Grad phi) operator + d_h1 = mfem.ParMixedBilinearForm(fes_cond_h1, fes_cond_rt) + d_h1.AddDomainIntegrator(mfem.MixedVectorGradientIntegrator(sigmaCoef)) + d_h1.Assemble() + + # Compute the r.h.s, b_rt = sigma E = -sigma Grad phi + b_rt = mfem.ParLinearForm(fes_cond_rt) + d_h1.Mult(phi_h1, b_rt) + b_rt *= -1.0 + + # Apply the necessary boundary conditions and solve for J in H(div) + glb_size_rt = fes_cond_rt.GlobalTrueVSize() + if myid == 0: + print("\nSolving for current density in H(Div), using diagonally scaled CG") + print("Size of linear system: " + str(glb_size_rt)) + + ess_bdr_tdof_rt = mfem.intArray() + M = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + + fes_cond_rt.GetEssentialTrueDofs(ess_bdr_j, ess_bdr_tdof_rt) + j_cond.Assign(0.0) + m_rt.FormLinearSystem(ess_bdr_tdof_rt, j_cond, b_rt, M, X, B) + + pred = mfem.HypreDiagScale() + cg = mfem.CGSolver(MPI.COMM_WORLD) + cg.SetRelTol(1e-12) + cg.SetMaxIter(2000) + cg.SetPrintLevel(1) + cg.SetPreconditioner(prec) + cg.SetOperator(M.Ptr()) + cg.Mult(B, X) + m_rt.RecoverFEMSolution(X, b_rt, j_cond) + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser( + description='Ex34p (Sourse Function using a Submehs Transfer )') + + parser.add_argument('-rs', '--refine-serial', + action='store', default=1, type=int, + help="Number of times to refine the mesh uniformly in serial.") + parser.add_argument('-rp', '--refine-parallel', + action='store', default=1, type=int, + help="Number of times to refine the mesh uniformly in parallel.") + parser.add_argument("-o", "--order", + action='store', default=1, type=int, + help="Finite element order (polynomial degree).") + parser.add_argument("-mc", "--magnetic-cond", + action='store', default=1e-6, type=float, + help="Magnetic Conductivity") + parser.add_argument("-sc", "--static-condensation", + action='store_true', + help="Enable static condensation.") + parser.add_argument("-hex", "--hex-mesh", + action='store_true', default=False, + help="Mixed mesh of hexahedral mesh.") + parser.add_argument("-pa", "--partial-assembly", + action='store_true', + help="Enable Partial Assembly.") + parser.add_argument("-d", "--device", + default="cpu", type=str, + help="Device configuration string, see Device::Configure().") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + + args = parser.parse_args() + if myid == 0: + parser.print_options(args) + + globals()["pa"] = args.partial_assembly + globals()["visualization"] = not args.no_visualization + + run(ser_ref_levels=args.refine_serial, + par_ref_levels=args.refine_parallel, + order=args.order, + delta_const=args.magnetic_cond, + static_cond=args.static_condensation, + mixed=(not args.hex_mesh), + device_config=args.device) diff --git a/examples/ex35p.py b/examples/ex35p.py new file mode 100644 index 00000000..b4cc47e6 --- /dev/null +++ b/examples/ex35p.py @@ -0,0 +1,680 @@ +''' + MFEM example 35p + See c++ version in the MFEM library for more detail + + Sample runs: mpirun -np 4 python ex35p.py -p 0 -o 2 + mpirun -np 4 python ex35p.py -p 0 -o 2 -pbc '22 23 24' -em 0 + mpirun -np 4 python ex35p.py -p 1 -o 1 -rp 2 + mpirun -np 4 python ex35p.py -p 1 -o 2 + mpirun -np 4 python ex35p.py -p 2 -o 1 -rp 2 -c 15 +''' +import os +import sys +import mfem.par as mfem +from mfem.par import intArray +from os.path import expanduser, join, dirname +import numpy as np +from numpy import sin, cos, exp, sqrt, pi +from mpi4py import MPI + +num_procs = MPI.COMM_WORLD.size +myid = MPI.COMM_WORLD.rank +smyid = '.'+'{:0>6d}'.format(myid) + +mixed = True +visualization = True +pa = False +slu_solver = False # SuperLU option not supported + + +def run(mesh_file="", + order=1, + ser_ref_levels=0, + par_ref_levels=0, + prob=0, + mode=1, + herm_conv=True, + epsilon=1.0, + sigma=2., + mu=1.0, + device='cpu', + port_bc_attr=None, + freq=-1.0,): + + mesh_file = "../data/fichera-mixed.mesh" + if not mixed or pa: + mesh_file = "../data/fichera.mesh" + + omega = 2*pi + if freq > 0.0: + omega = 2.0 * pi * freq + + if (len(port_bc_attr) == 0 and + (mesh_file == "../data/fichera-mixed.mesh" or + mesh_file == "../data/fichera.mesh")): + port_bc_attr = mfem.intArray([7, 8, 11, 12]) + + port_bc_attr.Print() + conv = mfem.ComplexOperator.HERMITIAN if herm_conv else mfem.ComplexOperator.BLOCK_SYMMETRIC + # 3. Enable hardware devices such as GPUs, and programming models such as + # CUDA, OCCA, RAJA and OpenMP based on command line options. + device = mfem.Device(device) + if myid == 0: + device.Print() + + # 4. Read the mesh from the given mesh file. We can handle triangular, + # quadrilateral, tetrahedral, hexahedral, surface and volume meshes + # with the same code. + mesh = mfem.Mesh(mesh_file, 1, 1) + dim = mesh.Dimension() + + # 5. Refine the serial mesh on all processors to increase the resolution. + for i in range(ser_ref_levels): + mesh.UniformRefinement() + + # 6a. Define a parallel mesh by a partitioning of the serial mesh. Refine + # this mesh further in parallel to increase the resolution. Once the + # parallel mesh is defined, the serial mesh can be deleted. + pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) + for i in range(par_ref_levels): + pmesh.UniformRefinement() + + # 6b. Extract a submesh covering a portion of the boundary + pmesh_port = mfem.ParSubMesh.CreateFromBoundary(pmesh, port_bc_attr) + + # 7a. Define a parallel finite element space on the parallel mesh. Here we + # use continuous Lagrange, Nedelec, or Raviart-Thomas finite elements + # of the specified order. + if dim == 1 and prob != 0: + if myid == 0: + print( + "Switching to problem type 0, H1 basis functions, for 1 dimensional mesh.") + prob = 0 + + if prob == 0: + fec = mfem.H1_FECollection(order, dim) + elif prob == 1: + fec = mfem.ND_FECollection(order, dim) + elif prob == 2: + fec = mfem.RT_FECollection(order-1, dim) + else: + assert False, "unknown problem" + fespace = mfem.ParFiniteElementSpace(pmesh, fec) + size = fespace.GlobalTrueVSize() + if myid == 0: + print("Number of finite element unknowns: " + str(size)) + + # 7b. Define a parallel finite element space on the sub-mesh. Here we + # use continuous Lagrange, Nedelec, or L2 finite elements of + # the specified order. + if prob == 0: + fec_port = mfem.H1_FECollection(order, dim-1) + elif prob == 1: + if dim == 3: + fec_port = mfem.ND_FECollection(order, dim-1) + else: + fec_port = mfem.L2_FECollection(order - 1, dim-1, + mfem.BasisType.GaussLegendre, + mfem.FiniteElement.INTEGRAL) + elif prob == 2: + fec_port = mfem.L2_FECollection(order - 1, dim-1, + mfem.BasisType.GaussLegendre, + mfem.FiniteElement.INTEGRAL) + else: + assert False, "should not reach here" + + fespace_port = mfem.ParFiniteElementSpace(pmesh_port, fec_port) + size_port = fespace_port.GlobalTrueVSize() + if myid == 0: + print("Number of finite element port BC unknowns: " + str(size_port)) + + # 8a. Define a parallel grid function on the SubMesh which will contain + # the field to be applied as a port boundary condition. + port_bc = mfem.ParGridFunction(fespace_port) + port_bc.Assign(0.0) + + SetPortBC(prob, dim, mode, port_bc) + + # 8b. Save the SubMesh and associated port boundary condition in parallel. + # This output can be viewed later using GLVis: + # "glvis -np -m port_mesh -g port_mode" + pmesh_port.Print("port_mesh"+smyid, 8) + port_bc.Save("port_mode"+smyid, 8) + + # 8c. Send the port bc, computed on the SubMesh, to a GLVis server. + if visualization and dim == 3: + port_sock = mfem.socketstream("localhost", 19916) + port_sock << "parallel " << num_procs << " " << myid << "\n" + port_sock.precision(8) + port_sock << "solution\n" << pmesh_port << port_bc + port_sock << "window_title 'Port BC'" + port_sock << "window_geometry 0 0 400 350" + port_sock.flush() + + # 9. Determine the list of true (i.e. parallel conforming) essential + # boundary dofs. In this example, the boundary conditions are defined + # using an eigenmode of the appropriate type computed on the SubMesh. + ess_tdof_list = mfem.intArray() + if pmesh.bdr_attributes.Size(): + ess_bdr = mfem.intArray([1]*pmesh.bdr_attributes.Max()) + fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list) + + # 10. Set up the parallel linear form b(.) which corresponds to the + # right-hand side of the FEM linear system. + b = mfem.ParComplexLinearForm(fespace, conv) + b.Assign(0.0) + + # 11a. Define the solution vector u as a parallel complex finite element + # grid function corresponding to fespace. Initialize u to equal zero. + u = mfem.ParComplexGridFunction(fespace) + u.Assign(0.0) + pmesh_port.Transfer(port_bc, u.real()) + + # 11b. Send the transferred port bc field to a GLVis server. + + full_bc = mfem.ParGridFunction(fespace) + port_to_full = mfem.ParTransferMap(port_bc, full_bc) + + full_bc.Assign(0.0) + port_to_full.Transfer(port_bc, full_bc) + + if visualization: + full_sock = mfem.socketstream("localhost", 19916) + full_sock << "parallel " << num_procs << " " << myid << "\n" + full_sock.precision(8) + full_sock << "solution\n" << pmesh << full_bc + full_sock << "window_title 'Transferred BC'" + full_sock << "window_geometry 400 0 400 350" + full_sock.flush() + + # 12. Set up the parallel sesquilinear form a(.,.) on the finite element + # space corresponding to the damped harmonic oscillator operator of the + # appropriate type: + # + # 0) A scalar H1 field + # -Div(a Grad) - omega^2 b + i omega c + # + # 1) A vector H(Curl) field + # Curl(a Curl) - omega^2 b + i omega c + # + # 2) A vector H(Div) field + # -Grad(a Div) - omega^2 b + i omega c + # + stiffnessCoef = mfem.ConstantCoefficient(1.0/mu) + massCoef = mfem.ConstantCoefficient(-omega * omega * epsilon) + lossCoef = mfem.ConstantCoefficient(omega * sigma) + negMassCoef = mfem.ConstantCoefficient(omega * omega * epsilon) + + a = mfem.ParSesquilinearForm(fespace, conv) + + if pa: + a.SetAssemblyLevel(mfem.AssemblyLevel_PARTIAL) + if prob == 0: + a.AddDomainIntegrator(mfem.DiffusionIntegrator(stiffnessCoef), + None) + a.AddDomainIntegrator(mfem.MassIntegrator(massCoef), + mfem.MassIntegrator(lossCoef)) + elif prob == 1: + a.AddDomainIntegrator(mfem.CurlCurlIntegrator(stiffnessCoef), + None) + a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(massCoef), + mfem.VectorFEMassIntegrator(lossCoef)) + elif prob == 2: + a.AddDomainIntegrator(mfem.DivDivIntegrator(stiffnessCoef), + None) + a.AddDomainIntegrator(mfem.VectorFEMassIntegrator(massCoef), + mfem.VectorFEMassIntegrator(lossCoef)) + else: + assert False, "Unknown probm" + + # 13. Assemble the parallel bilinear form and the corresponding linear + # system, applying any necessary transformations such as: parallel + # assembly, eliminating boundary conditions, applying conforming + # constraints for non-conforming AMR, etc. + a.Assemble() + A = mfem.OperatorHandle() + B = mfem.Vector() + U = mfem.Vector() + a.FormLinearSystem(ess_tdof_list, u, b, A, U, B) + + if myid == 0: + print("Size of linear system: " + str(2*size)) + + if not slu_solver: + # 14a. Set up the parallel bilinear form for the preconditioner + # corresponding to the appropriate operator + # + # 0) A scalar H1 field + # -Div(a Grad) - omega^2 b + i omega c + # + # 1) A vector H(Curl) field + # Curl(a Curl) + omega^2 b + i omega c + # + # 2) A vector H(Div) field + # -Grad(a Div) - omega^2 b + i omega c + pcOp = mfem.ParBilinearForm(fespace) + if pa: + pcOp.SetAssemblyLevel(mfem.AssemblyLevel_PARTIAL) + + if prob == 0: + pcOp.AddDomainIntegrator(mfem.DiffusionIntegrator(stiffnessCoef)) + pcOp.AddDomainIntegrator(mfem.MassIntegrator(massCoef)) + pcOp.AddDomainIntegrator(mfem.MassIntegrator(lossCoef)) + elif prob == 1: + pcOp.AddDomainIntegrator(mfem.CurlCurlIntegrator(stiffnessCoef)) + pcOp.AddDomainIntegrator(mfem.VectorFEMassIntegrator(negMassCoef)) + pcOp.AddDomainIntegrator(mfem.VectorFEMassIntegrator(lossCoef)) + elif prob == 2: + pcOp.AddDomainIntegrator(mfem.DivDivIntegrator(stiffnessCoef)) + pcOp.AddDomainIntegrator(mfem.VectorFEMassIntegrator(massCoef)) + pcOp.AddDomainIntegrator(mfem.VectorFEMassIntegrator(lossCoef)) + pcOp.Assemble() + + # 14b. Define and apply a parallel FGMRES solver for AU=B with a block + # diagonal preconditioner based on the appropriate multigrid + # preconditioner from hypre. + blockTrueOffsets = mfem.intArray() + blockTrueOffsets.SetSize(3) + blockTrueOffsets[0] = 0 + blockTrueOffsets[1] = A.Height() // 2 + blockTrueOffsets[2] = A.Height() // 2 + blockTrueOffsets.PartialSum() + + BDP = mfem.BlockDiagonalPreconditioner(blockTrueOffsets) + + if pa: + pc_r = mfem.OperatorJacobiSmoother(pcOp, ess_tdof_list) + pc_i = None + else: + PCOp = mfem.OperatorHandle() + pcOp.FormSystemMatrix(ess_tdof_list, PCOp) + if prob == 0: + pc_r = mfem.HypreBoomerAMG(PCOp.AsHypreParMatrix()) + elif prob == 1: + pc_r = mfem.HypreAMS(PCOp.AsHypreParMatrix(), fespace) + elif prob == 2: + if dim == 2: + pc_r = mfem.HypreAMS(PCOp.AsHypreParMatrix(), fespace) + else: + pc_r = mfem.HypreADS(PCOp.AsHypreParMatrix(), fespace) + + pc_i = mfem.ScaledOperator(pc_r, + -1 if conv == mfem.ComplexOperator.HERMITIAN else 1) + BDP.SetDiagonalBlock(0, pc_r) + BDP.SetDiagonalBlock(1, pc_i) + + fgmres = mfem.FGMRESSolver(MPI.COMM_WORLD) + fgmres.SetPreconditioner(BDP) + fgmres.SetOperator(A.Ptr()) + fgmres.SetRelTol(1e-6) + fgmres.SetMaxIter(1000) + fgmres.SetPrintLevel(1) + fgmres.Mult(B, U) + + # 15. Recover the parallel grid function corresponding to U. This is the + # local finite element solution on each processor. + a.RecoverFEMSolution(U, b, u) + + # 16. Save the refined mesh and the solution in parallel. This output can be + # viewed later using GLVis: "glvis -np -m mesh -g sol_r" or + # "glvis -np -m mesh -g sol_i". + pmesh.Print("mesh"+smyid, 8) + u.real().Save("sol_r"+smyid, 8) + u.imag().Save("sol_i"+smyid, 8) + + # 17. Send the solution by socket to a GLVis server. + if visualization: + sol_sock_r = mfem.socketstream("localhost", 19916) + sol_sock_r << "parallel " << num_procs << " " << myid << "\n" + sol_sock_r.precision(8) + sol_sock_r << "solution\n" << pmesh << u.real( + ) << "window_title 'Solution: Real Part'" + sol_sock_r << "window_geometry 800 0 400 350" + sol_sock_r.flush() + + sol_sock_i = mfem.socketstream("localhost", 19916) + sol_sock_i << "parallel " << num_procs << " " << myid << "\n" + sol_sock_i.precision(8) + sol_sock_i << "solution\n" << pmesh << u.imag( + ) << "window_title 'Solution: Imag Part'" + sol_sock_i << "window_geometry 1200 0 400 350" + sol_sock_i.flush() + + if visualization: + u_t = mfem.ParGridFunction(fespace) + u_t.Assign(u.real()) + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock << "parallel " << num_procs << " " << myid << "\n" + sol_sock.precision(8) + sol_sock << "solution\n" << pmesh << u_t + sol_sock << "window_title 'Harmonic Solution (t = 0.0 T)'" + sol_sock << "window_geometry 0 432 600 450" + sol_sock << "pause\n" + sol_sock.flush() + + if myid == 0: + print( + "GLVis visualization paused. Press space (in the GLVis window) to resume it.") + num_frames = 32 + i = 0 + + # Let's plot one wave cycle... + for i in range(160): + t = (i % num_frames) / num_frames + oss = "Harmonic Solution (t = " + str(t) + " T)" + dd = (cos(2.0 * pi * t)*u.real().GetDataArray() + + sin(2.0 * pi * t)*u.imag().GetDataArray()) + # we can not load numpy directly...(sorry) + u_t.Assign(mfem.Vector(dd)) + sol_sock << "parallel " << num_procs << " " << myid << "\n" + sol_sock << "solution\n" << pmesh << u_t + sol_sock << "window_title '" << oss << "'" + sol_sock.flush() + + +''' + Solves the eigenvalue problem -Div(Grad x) = lambda x with homogeneous + Dirichlet boundary conditions on the boundary of the domain. Returns mode + number "mode" (counting from zero) in the ParGridFunction "x". +''' + + +def ScalarWaveGuide(mode, x): + nev = max(mode + 2, 5) + seed = 75 + + fespace = x.ParFESpace() + pmesh = fespace.GetParMesh() + + if pmesh.bdr_attributes.Size() > 0: + ess_bdr = mfem.intArray([1]*pmesh.bdr_attributes.Max()) + else: + ess_bdr = mfem.intArray() + + a = mfem.ParBilinearForm(fespace) + a.AddDomainIntegrator(mfem.DiffusionIntegrator()) + a.Assemble() + a.EliminateEssentialBCDiag(ess_bdr, 1.0) + a.Finalize() + + m = mfem.ParBilinearForm(fespace) + m.AddDomainIntegrator(mfem.MassIntegrator()) + m.Assemble() + + # shift the eigenvalue corresponding to eliminated dofs to a large value + m.EliminateEssentialBCDiag(ess_bdr, sys.float_info.min) + m.Finalize() + + A = a.ParallelAssemble() + M = m.ParallelAssemble() + + amg = mfem.HypreBoomerAMG(A) + amg.SetPrintLevel(0) + + lobpcg = mfem.HypreLOBPCG(MPI.COMM_WORLD) + lobpcg.SetNumModes(nev) + lobpcg.SetRandomSeed(seed) + lobpcg.SetPreconditioner(amg) + lobpcg.SetMaxIter(200) + lobpcg.SetTol(1e-8) + lobpcg.SetPrecondUsageMode(1) + lobpcg.SetPrintLevel(1) + lobpcg.SetMassMatrix(M) + lobpcg.SetOperator(A) + lobpcg.Solve() + + x.Assign(lobpcg.GetEigenvector(mode)) + + +''' + Solves the eigenvalue problem -Curl(Curl x) = lambda x with homogeneous + Dirichlet boundary conditions, on the tangential component of x, on the + boundary of the domain. Returns mode number "mode" (counting from zero) in + the ParGridFunction "x". +''' + + +def VectorWaveGuide(mode, x): + nev = max(mode + 2, 5) + fespace = x.ParFESpace() + pmesh = fespace.GetParMesh() + + if pmesh.bdr_attributes.Size() > 0: + ess_bdr = mfem.intArray([1]*pmesh.bdr_attributes.Max()) + else: + ess_bdr = mfem.intArray() + + a = mfem.ParBilinearForm(fespace) + a.AddDomainIntegrator(mfem.CurlCurlIntegrator()) + a.Assemble() + a.EliminateEssentialBCDiag(ess_bdr, 1.0) + a.Finalize() + + m = mfem.ParBilinearForm(fespace) + m.AddDomainIntegrator(mfem.VectorFEMassIntegrator()) + m.Assemble() + + # shift the eigenvalue corresponding to eliminated dofs to a large value + m.EliminateEssentialBCDiag(ess_bdr, sys.float_info.min) + m.Finalize() + + A = a.ParallelAssemble() + M = m.ParallelAssemble() + + ams = mfem.HypreAMS(A, fespace) + ams.SetPrintLevel(0) + ams.SetSingularProblem() + + ame = mfem.HypreAME(MPI.COMM_WORLD) + ame.SetNumModes(nev) + ame.SetPreconditioner(ams) + ame.SetMaxIter(100) + ame.SetTol(1e-8) + ame.SetPrintLevel(1) + ame.SetMassMatrix(M) + ame.SetOperator(A) + ame.Solve() + + x.Assign(ame.GetEigenvector(mode)) + + +''' + Solves the eigenvalue problem -Div(Grad x) = lambda x with homogeneous + Neumann boundary conditions on the boundary of the domain. Returns mode + number "mode" (counting from zero) in the ParGridFunction "x_l2". Note that + mode 0 is a constant field so higher mode numbers are often more + interesting. The eigenmode is solved using continuous H1 basis of the + appropriate order and then projected onto the L2 basis and returned. +''' + + +def PseudoScalarWaveGuide(mode, x_l2): + nev = max(mode + 2, 5) + seed = 75 + + fespace_l2 = x_l2.ParFESpace() + pmesh = fespace_l2.GetParMesh() + order_l2 = fespace_l2.FEColl().GetOrder() + + fec = mfem.H1_FECollection(order_l2+1, pmesh.Dimension()) + fespace = mfem.ParFiniteElementSpace(pmesh, fec) + x = mfem.ParGridFunction(fespace) + x.Assign(0.0) + + xCoef = mfem.GridFunctionCoefficient(x) + if mode == 0: + x.Assign(1.0) + x_l2.ProjectCoefficient(xCoef) + + a = mfem.ParBilinearForm(fespace) + a.AddDomainIntegrator(mfem.DiffusionIntegrator()) + a.AddDomainIntegrator(mfem.MassIntegrator()) + a.Assemble() + a.Finalize() + + m = mfem.ParBilinearForm(fespace) + m.AddDomainIntegrator(mfem.MassIntegrator()) + m.Assemble() + m.Finalize() + + A = a.ParallelAssemble() + M = m.ParallelAssemble() + + amg = mfem.HypreBoomerAMG(A) + amg.SetPrintLevel(0) + + lobpcg = mfem.HypreLOBPCG(MPI.COMM_WORLD) + lobpcg.SetNumModes(nev) + lobpcg.SetRandomSeed(seed) + lobpcg.SetPreconditioner(amg) + lobpcg.SetMaxIter(200) + lobpcg.SetTol(1e-8) + lobpcg.SetPrecondUsageMode(1) + lobpcg.SetPrintLevel(1) + lobpcg.SetMassMatrix(M) + lobpcg.SetOperator(A) + lobpcg.Solve() + + x.Assign(lobpcg.GetEigenvector(mode)) + x_l2.ProjectCoefficient(xCoef) + +# Compute eigenmode "mode" of either a Dirichlet or Neumann Laplacian or of a +# Dirichlet curl curl operator based on the problem type and dimension of the +# domain. + + +def SetPortBC(prob, dim, mode, port_bc): + if prob == 0: + ScalarWaveGuide(mode, port_bc) + elif prob == 1: + if dim == 3: + VectorWaveGuide(mode, port_bc) + else: + PseudoScalarWaveGuide(mode, port_bc) + elif prob == 2: + PseudoScalarWaveGuide(mode, port_bc) + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser( + description='Ex35p (Port Boundary Conditions using SubMesh Transfers)') + parser.add_argument('-m', '--mesh', + default='inline-quad.mesh', + action='store', type=str, + help='Mesh file to use.') + parser.add_argument("-rs", "--refine-serial", + action='store', type=int, default=1, + help="Number of times to refine the mesh uniformly in serial.") + parser.add_argument("-rp", "--refine-parallel", + action='store', type=int, default=1, + help="Number of times to refine the mesh uniformly in paralle.") + parser.add_argument('-o', '--order', + action='store', default=1, type=int, + help="Finite element order (polynomial degree)") + parser.add_argument("-p", "--problem-type", + action='store', type=int, default=0, + help="\n".join(["Choose between 0: H_1, 1: H(Curl), or 2: H(Div) " + "damped harmonic oscillator."])) + parser.add_argument("-em", "--eigenmode", + action='store', type=int, default=1, + help="Choose the index of the port eigenmode.") + parser.add_argument("-a", "--stiffness-coef", + action='store', type=float, default=0.0, + help="Stiffness coefficient (spring constant or 1/mu).") + parser.add_argument("-b", "--mass-coef", + action='store', type=float, default=1.0, + help="Mass coefficient (or epsilon).") + parser.add_argument("-c", "--damping-coef", + action='store', type=float, default=2.0, + help="Damping coefficient (or sigma).") + parser.add_argument("-mu", "--permeability", + action='store', type=float, default=1.0, + help="Permeability of free space (or 1/(spring constant)).") + parser.add_argument("-eps", "--permittivity", + action='store', type=float, default=1.0, + help="Permittivity of free space (or mass constant).") + parser.add_argument("-sigma", "--conductivity", + action='store', type=float, default=2.0, + help="Conductivity (or damping constant).") + parser.add_argument("-f", "--frequency", + action='store', + type=float, + default=-1.0, + help="Set the frequency for the exact") + parser.add_argument("-pbc", "--port-bc-attr", + action='store', type=str, default="", + help="Attributes of port boundary condition") + parser.add_argument("-herm", "--hermitian", + action='store_true', + default=True, + help="Do not use convention for Hermitian operators.") + parser.add_argument("-no-herm", "--no-hermitian", + action='store_true', + default=False, + help="Do not use convention for Hermitian operators.") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + parser.add_argument("-hex", "--hex-mesh", + action='store_true', default=False, + help="Mixed mesh of hexahedral mesh.") + parser.add_argument("-pa", "--partial-assembly", + action='store_true', + help="Enable Partial Assembly.") + parser.add_argument("-d", "--device", + default="cpu", type=str, + help="Device configuration string, see Device::Configure().") + + args = parser.parse_args() + + herm = False if args.no_hermitian else True + args.hermitian = herm + args.no_hermitian = not herm + + if myid == 0: + parser.print_options(args) + + meshfile = expanduser( + join(os.path.dirname(__file__), '..', 'data', args.mesh)) + + port_bc_attr = [int(x) for x in args.port_bc_attr.split(' ') if len(x) > 0] + globals()["mixed"] = not args.hex_mesh + globals()["pa"] = args.partial_assembly + globals()["visualization"] = not args.no_visualization + + if args.stiffness_coef != 0.0: + mu = 1.0/args.stiffness_coef + elif args.permeability != 1.0: + mu = args.permeability + else: + mu = 1.0 + + if args.permittivity != 1.0: + epsilon = args.permittivity + elif args.mass_coef != 1.0: + epsilon = args.mass_coef + else: + epsilon = 1.0 + + if args.conductivity != 2.0: + sigma = args.conductivity + elif args.damping_coef != 2.0: + sigma = args.damping_coef + else: + sigma = 2.0 + + run(mesh_file=meshfile, + order=args.order, + ser_ref_levels=args.refine_serial, + par_ref_levels=args.refine_parallel, + prob=args.problem_type, + mode=args.eigenmode, + herm_conv=herm, + epsilon=epsilon, + sigma=sigma, + mu=mu, + device=args.device, + port_bc_attr=port_bc_attr, + freq=args.frequency) diff --git a/examples/ex36.py b/examples/ex36.py new file mode 100644 index 00000000..ec814068 --- /dev/null +++ b/examples/ex36.py @@ -0,0 +1,407 @@ +''' + PyMFEM example 36 + + See c++ version in the MFEM library for more detail + + Sample runs: + mpirun -np 4 python ex36.py -o 2 + mpirun -np 4 python ex36.py -o 2 -r 4 + + +''' +import os +from os.path import expanduser, join + +from numpy import sqrt, log, exp +import numpy as np +from numba import njit +from numba.types import float64 + + +import mfem.ser as mfem +from mfem.ser import intArray, doubleArray + + +visualization = True + + +def run(refs=3, + order=1, + max_it=10, + tol=1e-5, + alpha=1.0): + + # 2. Read the mesh from the mesh file. + mesh_file = "../data/disc-nurbs.mesh" + mesh_file = expanduser( + join(os.path.dirname(__file__), *mesh_file.split("/"))) + mesh = mfem.Mesh(mesh_file, 1, 1) + dim = mesh.Dimension() + + # 3. Postprocess the mesh. + # 3A. Refine the mesh to increase the resolution. + for l in range(refs): + mesh.UniformRefinement() + + # 3B. Interpolate the geometry after refinement to control geometry error. + # NOTE: Minimum second-order interpolation is used to improve the accuracy. + curvature_order = max((order, 2)) + mesh.SetCurvature(curvature_order) + + # 3C. Rescale the domain to a unit circle (radius = 1). + nodes = mesh.GetNodes() + scale = 2*sqrt(2) + nodes /= scale + + # 4. Define the necessary finite element spaces on the mesh. + H1fec = mfem.H1_FECollection(order+1, dim) + H1fes = mfem.FiniteElementSpace(mesh, H1fec) + + L2fec = mfem.L2_FECollection(order-1, dim) + L2fes = mfem.FiniteElementSpace(mesh, L2fec) + + print("Number of H1 finite element unknowns: " + + str(H1fes.GetTrueVSize())) + print("Number of L2 finite element unknowns: " + + str(L2fes.GetTrueVSize())) + + offsets = mfem.intArray((0, H1fes.GetVSize(), L2fes.GetVSize())) + offsets.PartialSum() + + x = mfem.BlockVector(offsets) + rhs = mfem.BlockVector(offsets) + x.Assign(0.0) + rhs.Assign(0.0) + + # 5. Determine the list of true (i.e. conforming) essential boundary dofs. + if mesh.bdr_attributes.Size() > 0: + ess_bdr = mfem.intArray([1]*mesh.bdr_attributes.Max()) + else: + ess_bdr = mfem.intArray() + + # 6. Define an initial guess for the solution. + @njit(float64(float64[:])) + def IC_func(x): + r0 = 1.0 + rr = 0.0 + for i in range(len(x)): + rr += x[i]*x[i] + return r0*r0 - rr + + one = mfem.ConstantCoefficient(1.0) + zero = mfem.ConstantCoefficient(0.0) + + # 7. Define the solution vectors as a finite element grid functions + # corresponding to the fespaces. + u_gf = mfem.GridFunction() + delta_psi_gf = mfem.GridFunction() + u_gf.MakeRef(H1fes, x, offsets[0]) + delta_psi_gf.MakeRef(L2fes, x, offsets[1]) + delta_psi_gf.Assign(0.0) + + u_old_gf = mfem.GridFunction(H1fes) + psi_old_gf = mfem.GridFunction(L2fes) + psi_gf = mfem.GridFunction(L2fes) + u_old_gf.Assign(0.0) + psi_old_gf.Assign(0.0) + + # 8. Define the function coefficients for the solution and use them to + # initialize the initial guess + @mfem.jit.scalar + def exact_coef(ptx): + return exact_solution_obstacle(ptx[0], ptx[1]) + + @mfem.jit.vector(shape=(dim, )) + def exact_grad_coef(ptx): + return exact_solution_gradient_obstacle(ptx[0], ptx[1]) + + @mfem.jit.scalar + def IC_coef(ptx): + return IC_func(ptx) + f = mfem.ConstantCoefficient(0.0) + + @mfem.jit.scalar + def obstacle(ptx): + return spherical_obstacle(ptx[0], ptx[1]) + + u_gf.ProjectCoefficient(IC_coef) + u_old_gf.GetDataArray()[:] = u_gf.GetDataArray() + + # 9. Initialize the slack variable ψₕ = ln(uₕ) + c_u_gf = mfem.GridFunctionCoefficient(u_gf) + + @mfem.jit.scalar(dependency=(c_u_gf, obstacle)) + def ln_u(ptx, u, obstacle): + min_val = -36. + val = u - obstacle + return max((min_val, log(val))) + + psi_gf.ProjectCoefficient(ln_u) + psi_old_gf.GetDataArray()[:] = psi_gf.GetDataArray() + + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock.precision(8) + + # Note: we define exp_psi outside the iteration loop to avoid + # numba-jit during the loop. + # GridFunction referred from c_psi_gf is updated during + # the iteration. + c_psi_gf = mfem.GridFunctionCoefficient() + + @mfem.jit.scalar(dependency=(c_psi_gf, )) + def exp_psi(ptx, val): + min_val = 0 + max_val = 1e36 + return min(max_val, max(min_val, exp(val))) + + # 10. Iterate + total_iterations = 0 + increment_u = 0.1 + for k in range(max_it): + u_tmp = mfem.GridFunction(H1fes) + u_tmp.GetDataArray()[:] = u_old_gf.GetDataArray() + + print("\nOUTER ITERATION " + str(k+1)) + + for j in range(10): + total_iterations += 1 + + alpha_cf = mfem.ConstantCoefficient(alpha) + + b0 = mfem.LinearForm() + b1 = mfem.LinearForm() + b0.Update(H1fes, rhs.GetBlock(0), 0) + b1.Update(L2fes, rhs.GetBlock(1), 0) + + c_psi_gf.SetGridFunction(psi_gf) + neg_exp_psi = mfem.ProductCoefficient(-1.0, exp_psi) + grad_u_old = mfem.GradientGridFunctionCoefficient(u_old_gf) + alpha_f = mfem.ProductCoefficient(alpha, f) + psi_cf = mfem.GridFunctionCoefficient(psi_gf) + psi_old_cf = mfem.GridFunctionCoefficient(psi_old_gf) + psi_old_minus_psi = mfem.SumCoefficient( + psi_old_cf, psi_cf, 1.0, -1.0) + + b0.AddDomainIntegrator(mfem.DomainLFIntegrator(alpha_f)) + b0.AddDomainIntegrator(mfem.DomainLFIntegrator(psi_old_minus_psi)) + b0.Assemble() + + b1.AddDomainIntegrator(mfem.DomainLFIntegrator(exp_psi)) + b1.AddDomainIntegrator(mfem.DomainLFIntegrator(obstacle)) + b1.Assemble() + + a00 = mfem.BilinearForm(H1fes) + a00.SetDiagonalPolicy(mfem.Operator.DIAG_ONE) + a00.AddDomainIntegrator(mfem.DiffusionIntegrator(alpha_cf)) + a00.Assemble() + a00.EliminateEssentialBC(ess_bdr, x.GetBlock(0), rhs.GetBlock(0), + mfem.Operator.DIAG_ONE) + a00.Finalize() + A00 = a00.SpMat() + + a10 = mfem.MixedBilinearForm(H1fes, L2fes) + a10.AddDomainIntegrator(mfem.MixedScalarMassIntegrator()) + a10.Assemble() + a10.EliminateTrialDofs(ess_bdr, x.GetBlock(0), rhs.GetBlock(1)) + a10.Finalize() + A10 = a10.SpMat() + + A01 = mfem.Transpose(A10) + + a11 = mfem.BilinearForm(L2fes) + a11.AddDomainIntegrator(mfem.MassIntegrator(neg_exp_psi)) + # NOTE: Shift the spectrum of the Hessian matrix for additional + # stability (Quasi-Newton). + eps_cf = mfem.ConstantCoefficient(-1e-6) + if (order == 1): + # NOTE: ∇ₕuₕ = 0 for constant functions. + # Therefore, we use the mass matrix to shift the spectrum + a11.AddDomainIntegrator(mfem.MassIntegrator(eps_cf)) + else: + a11.AddDomainIntegrator(mfem.DiffusionIntegrator(eps_cf)) + + a11.Assemble() + a11.Finalize() + A11 = a11.SpMat() + + A = mfem.BlockOperator(offsets) + A.SetBlock(0, 0, A00) + A.SetBlock(1, 0, A10) + A.SetBlock(0, 1, A01) + A.SetBlock(1, 1, A11) + + prec = mfem.BlockDiagonalPreconditioner(offsets) + gs1 = mfem.GSSmoother(A00) + gs2 = mfem.GSSmoother(A11) + prec.SetDiagonalBlock(0, gs1) + prec.SetDiagonalBlock(1, gs2) + prec.owns_blocks = 0 + + mfem.GMRES(A, prec, rhs, x, 0, 10000, 500, 1e-12, 0.0) + + u_gf.MakeRef(H1fes, x.GetBlock(0), 0) + delta_psi_gf.MakeRef(L2fes, x.GetBlock(1), 0) + + u_tmp -= u_gf + Newton_update_size = u_tmp.ComputeL2Error(zero) + u_tmp.Assign(u_gf) + # Note: to copy GridFunction data, use either Assign or + # numpy representation. + # u_tmp.Assign(u_gf) + # u_tmp.GetDataArray()[:] = u_gf.GetDataArray() + + gamma = 1.0 + delta_psi_gf *= gamma + psi_gf += delta_psi_gf + + if visualization: + sol_sock << "solution\n" << mesh << u_gf + sol_sock << "window_title 'Discrete solution'" + sol_sock.flush() + print("Newton_update_size = " + + "{:g}".format(Newton_update_size)) + + del A01 + + if Newton_update_size < increment_u: + break + + u_tmp.GetDataArray()[:] = u_gf.GetDataArray() + u_tmp -= u_old_gf + increment_u = u_tmp.ComputeL2Error(zero) + + print("Number of Newton iterations = " + str(j+1)) + print("Increment (|| uₕ - uₕ_prvs||) = " + "{:g}".format(increment_u)) + + u_old_gf.GetDataArray()[:] = u_gf.GetDataArray() + psi_old_gf.GetDataArray()[:] = psi_gf.GetDataArray() + + if increment_u < tol or k == max_it-1: + break + + H1_error = u_gf.ComputeH1Error(exact_coef, exact_grad_coef) + print("H1-error (|| u - uₕᵏ||) = " + "{:g}".format(H1_error)) + + print("Outer iterations: " + str(k+1)) + print(" Total iterations: " + str(total_iterations)) + print(" Total dofs: " + str(H1fes.GetTrueVSize() + L2fes.GetTrueVSize())) + + # 11. Exact solution. + if visualization: + err_sock = mfem.socketstream("localhost", 19916) + err_sock.precision(8) + + error_gf = mfem.GridFunction(H1fes) + error_gf.ProjectCoefficient(exact_coef) + error_gf -= u_gf + + err_sock << "solution\n" << mesh << error_gf << "window_title 'Error'" + err_sock.flush() + + L2_error = u_gf.ComputeL2Error(exact_coef) + H1_error = u_gf.ComputeH1Error(exact_coef, exact_grad_coef) + + c_psi_gf = mfem.GridFunctionCoefficient(psi_gf) + + @mfem.jit.scalar(dependency=(c_psi_gf, obstacle)) + def u_alt_cf(ptx, val, obstacle): + min_val = 0 + max_val = 1e36 + return min(max_val, max(min_val, exp(val)+obstacle)) + + u_alt_gf = mfem.GridFunction(L2fes) + u_alt_gf.ProjectCoefficient(u_alt_cf) + L2_error_alt = u_alt_gf.ComputeL2Error(exact_coef) + + print("\n Final L2-error (|| u - uₕ||) = " + + "{:g}".format(L2_error)) + print(" Final H1-error (|| u - uₕ||) = " + + "{:g}".format(H1_error)) + print(" Final L2-error (|| u - ϕ - exp(ψₕ)||) = " + + "{:g}".format(L2_error_alt)) + + +@njit(float64(float64, float64)) +def spherical_obstacle(x, y): + r = sqrt(x*x + y*y) + r0 = 0.5 + beta = 0.9 + + b = r0*beta + tmp = sqrt(r0*r0 - b*b) + B = tmp + b*b/tmp + C = -b/tmp + + if r > b: + return B + r * C + else: + return sqrt(r0*r0 - r*r) + + +@njit(float64(float64, float64)) +def exact_solution_obstacle(x, y): + r = sqrt(x*x + y*y) + r0 = 0.5 + a = 0.348982574111686 + A = -0.340129705945858 + + if r > a: + return A * log(r) + else: + return sqrt(r0*r0-r*r) + + +@njit(float64[:](float64, float64)) +def exact_solution_gradient_obstacle(x, y): + r = sqrt(x*x + y*y) + r0 = 0.5 + a = 0.348982574111686 + A = -0.340129705945858 + + grad = np.zeros(2, dtype=np.float64) + if r > a: + grad[0] = A * x / (r*r) + grad[1] = A * y / (r*r) + else: + grad[0] = - x / sqrt(r0*r0 - r*r) + grad[1] = - y / sqrt(r0*r0 - r*r) + return grad + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser(description='Ex36 (Obstacle problem)') + + parser.add_argument("-o", "--order", + action='store', default=1, type=int, + help="Finite element order (polynomial degree).") + parser.add_argument('-r', '--refs', + action='store', default=3, type=int, + help="Number of times to refine the mesh uniformly.") + parser.add_argument('-mi', '--max-it', + action='store', default=10, type=int, + help="Maximum number of iterations") + help = "\n".join(("Stopping criteria based on the difference between", + "successive solution updates")) + parser.add_argument('-tol', '--tol', + action='store', default=1e-5, type=float, + help=help) + parser.add_argument('-step', '--step', + action='store', default=1.0, type=float, + help="Step size alpha") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + + args = parser.parse_args() + parser.print_options(args) + + globals()["visualization"] = not args.no_visualization + + run(refs=args.refs, + order=args.order, + max_it=args.max_it, + tol=args.tol, + alpha=args.step) diff --git a/examples/ex36p.py b/examples/ex36p.py new file mode 100644 index 00000000..518e6b7d --- /dev/null +++ b/examples/ex36p.py @@ -0,0 +1,442 @@ +''' + PyMFEM example 36p + + See c++ version in the MFEM library for more detail + + Sample runs: python ex36.py -o 2 + python ex36.py -o 2 -r 4 + + +''' +import os +from os.path import expanduser, join + +from numpy import sqrt, log, exp +import numpy as np +from numba import njit +from numba.types import float64 + + +import mfem.par as mfem +from mfem.par import intArray, doubleArray +from mpi4py import MPI + +num_procs = MPI.COMM_WORLD.size +myid = MPI.COMM_WORLD.rank +smyid = '{:0>6d}'.format(myid) + +visualization = True + + +def run(refs=3, + order=1, + max_it=10, + tol=1e-5, + alpha=1.0): + + # 2. Read the mesh from the mesh file. + mesh_file = "../data/disc-nurbs.mesh" + mesh_file = expanduser( + join(os.path.dirname(__file__), *mesh_file.split("/"))) + mesh = mfem.Mesh(mesh_file, 1, 1) + dim = mesh.Dimension() + + # 3. Postprocess the mesh. + # 3A. Refine the mesh to increase the resolution. + for l in range(refs): + mesh.UniformRefinement() + + # 3B. Interpolate the geometry after refinement to control geometry error. + # NOTE: Minimum second-order interpolation is used to improve the accuracy. + curvature_order = max((order, 2)) + mesh.SetCurvature(curvature_order) + + # 3C. Rescale the domain to a unit circle (radius = 1). + nodes = mesh.GetNodes() + scale = 2*sqrt(2) + nodes /= scale + + pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) + mesh.Clear() + + # 4. Define the necessary finite element spaces on the mesh. + H1fec = mfem.H1_FECollection(order+1, dim) + H1fes = mfem.ParFiniteElementSpace(pmesh, H1fec) + + L2fec = mfem.L2_FECollection(order-1, dim) + L2fes = mfem.ParFiniteElementSpace(pmesh, L2fec) + + num_dofs_H1 = H1fes.GlobalTrueVSize() + num_dofs_L2 = L2fes.GlobalTrueVSize() + if myid == 0: + print("Number of H1 finite element unknowns: " + str(num_dofs_H1)) + print("Number of L2 finite element unknowns: " + str(num_dofs_L2)) + + offsets = mfem.intArray((0, H1fes.GetVSize(), L2fes.GetVSize())) + offsets.PartialSum() + toffsets = mfem.intArray((0, H1fes.GetTrueVSize(), L2fes.GetTrueVSize())) + toffsets.PartialSum() + + x = mfem.BlockVector(offsets) + rhs = mfem.BlockVector(offsets) + x.Assign(0.0) + rhs.Assign(0.0) + tx = mfem.BlockVector(toffsets) + trhs = mfem.BlockVector(toffsets) + tx.Assign(0.0) + trhs.Assign(0.0) + + # 5. Determine the list of true (i.e. conforming) essential boundary dofs. + empty = mfem.intArray() + ess_tdof_list = mfem.intArray() + if pmesh.bdr_attributes.Size() > 0: + ess_bdr = mfem.intArray([1]*pmesh.bdr_attributes.Max()) + H1fes.GetEssentialTrueDofs(ess_bdr, ess_tdof_list) + + # 6. Define an initial guess for the solution. + @njit(float64(float64[:])) + def IC_func(x): + r0 = 1.0 + rr = 0.0 + for i in range(len(x)): + rr += x[i]*x[i] + return r0*r0 - rr + + one = mfem.ConstantCoefficient(1.0) + zero = mfem.ConstantCoefficient(0.0) + + # 7. Define the solution vectors as a finite element grid functions + # corresponding to the fespaces. + u_gf = mfem.ParGridFunction() + delta_psi_gf = mfem.ParGridFunction() + u_gf.MakeRef(H1fes, x, offsets[0]) + delta_psi_gf.MakeRef(L2fes, x, offsets[1]) + delta_psi_gf.Assign(0.0) + + u_old_gf = mfem.ParGridFunction(H1fes) + psi_old_gf = mfem.ParGridFunction(L2fes) + psi_gf = mfem.ParGridFunction(L2fes) + u_old_gf.Assign(0.0) + psi_old_gf.Assign(0.0) + + # 8. Define the function coefficients for the solution and use them to + # initialize the initial guess + @mfem.jit.scalar + def exact_coef(ptx): + return exact_solution_obstacle(ptx[0], ptx[1]) + + @mfem.jit.vector(shape=(dim, )) + def exact_grad_coef(ptx): + return exact_solution_gradient_obstacle(ptx[0], ptx[1]) + + @mfem.jit.scalar + def IC_coef(ptx): + return IC_func(ptx) + f = mfem.ConstantCoefficient(0.0) + + @mfem.jit.scalar + def obstacle(ptx): + return spherical_obstacle(ptx[0], ptx[1]) + + u_gf.ProjectCoefficient(IC_coef) + u_old_gf.GetDataArray()[:] = u_gf.GetDataArray() + + # 9. Initialize the slack variable ψₕ = ln(uₕ) + c_u_gf = mfem.GridFunctionCoefficient(u_gf) + + @mfem.jit.scalar(dependency=(c_u_gf, obstacle)) + def ln_u(ptx, u, obstacle): + min_val = -36. + val = u - obstacle + return max((min_val, log(val))) + + psi_gf.ProjectCoefficient(ln_u) + psi_old_gf.GetDataArray()[:] = psi_gf.GetDataArray() + + if visualization: + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock.precision(8) + + # Note: we define exp_psi outside the iteration loop to avoid + # numba-jit during the loop. + # GridFunction referred from c_psi_gf is updated during + # the iteration. + c_psi_gf = mfem.GridFunctionCoefficient() + + @mfem.jit.scalar(dependency=(c_psi_gf, )) + def exp_psi(ptx, val): + min_val = 0 + max_val = 1e36 + return min(max_val, max(min_val, exp(val))) + + # 10. Iterate + total_iterations = 0 + increment_u = 0.1 + for k in range(max_it): + u_tmp = mfem.ParGridFunction(H1fes) + u_tmp.GetDataArray()[:] = u_old_gf.GetDataArray() + + if myid == 0: + print("\nOUTER ITERATION " + str(k+1)) + + for j in range(10): + total_iterations += 1 + + alpha_cf = mfem.ConstantCoefficient(alpha) + + b0 = mfem.ParLinearForm() + b1 = mfem.ParLinearForm() + b0.Update(H1fes, rhs.GetBlock(0), 0) + b1.Update(L2fes, rhs.GetBlock(1), 0) + + c_psi_gf.SetGridFunction(psi_gf) + neg_exp_psi = mfem.ProductCoefficient(-1.0, exp_psi) + grad_u_old = mfem.GradientGridFunctionCoefficient(u_old_gf) + alpha_f = mfem.ProductCoefficient(alpha, f) + psi_cf = mfem.GridFunctionCoefficient(psi_gf) + psi_old_cf = mfem.GridFunctionCoefficient(psi_old_gf) + psi_old_minus_psi = mfem.SumCoefficient( + psi_old_cf, psi_cf, 1.0, -1.0) + + b0.AddDomainIntegrator(mfem.DomainLFIntegrator(alpha_f)) + b0.AddDomainIntegrator(mfem.DomainLFIntegrator(psi_old_minus_psi)) + b0.Assemble() + + b1.AddDomainIntegrator(mfem.DomainLFIntegrator(exp_psi)) + b1.AddDomainIntegrator(mfem.DomainLFIntegrator(obstacle)) + b1.Assemble() + + a00 = mfem.ParBilinearForm(H1fes) + a00.SetDiagonalPolicy(mfem.Operator.DIAG_ONE) + a00.AddDomainIntegrator(mfem.DiffusionIntegrator(alpha_cf)) + a00.Assemble() + A00 = mfem.HypreParMatrix() + a00.FormLinearSystem(ess_tdof_list, x.GetBlock(0), rhs.GetBlock(0), + A00, tx.GetBlock(0), trhs.GetBlock(0)) + + a10 = mfem.ParMixedBilinearForm(H1fes, L2fes) + a10.AddDomainIntegrator(mfem.MixedScalarMassIntegrator()) + a10.Assemble() + A10 = mfem.HypreParMatrix() + a10.FormRectangularLinearSystem(ess_tdof_list, empty, x.GetBlock(0), + rhs.GetBlock(1), + A10, tx.GetBlock(0), trhs.GetBlock(1)) + + A01 = A10.Transpose() + + a11 = mfem.ParBilinearForm(L2fes) + a11.AddDomainIntegrator(mfem.MassIntegrator(neg_exp_psi)) + # NOTE: Shift the spectrum of the Hessian matrix for additional + # stability (Quasi-Newton). + eps_cf = mfem.ConstantCoefficient(-1e-6) + if (order == 1): + # NOTE: ∇ₕuₕ = 0 for constant functions. + # Therefore, we use the mass matrix to shift the spectrum + a11.AddDomainIntegrator(mfem.MassIntegrator(eps_cf)) + else: + a11.AddDomainIntegrator(mfem.DiffusionIntegrator(eps_cf)) + + a11.Assemble() + A11 = mfem.HypreParMatrix() + a11.FormSystemMatrix(empty, A11) + + A = mfem.BlockOperator(toffsets) + A.SetBlock(0, 0, A00) + A.SetBlock(1, 0, A10) + A.SetBlock(0, 1, A01) + A.SetBlock(1, 1, A11) + + prec = mfem.BlockDiagonalPreconditioner(toffsets) + P00 = mfem.HypreBoomerAMG(A00) + P11 = mfem.HypreBoomerAMG(A11) + P00.SetPrintLevel(0) + P11.SetPrintLevel(0) + prec.SetDiagonalBlock(0, P00) + prec.SetDiagonalBlock(1, P11) + prec.owns_blocks = 0 + + gmres = mfem.GMRESSolver(MPI.COMM_WORLD) + gmres.SetPrintLevel(-1) + gmres.SetRelTol(1e-8) + gmres.SetMaxIter(20000) + gmres.SetKDim(500) + gmres.SetOperator(A) + gmres.SetPreconditioner(prec) + gmres.Mult(trhs, tx) + + u_gf.SetFromTrueDofs(tx.GetBlock(0)) + delta_psi_gf.SetFromTrueDofs(tx.GetBlock(1)) + + u_tmp -= u_gf + Newton_update_size = u_tmp.ComputeL2Error(zero) + u_tmp.Assign(u_gf) + # Note: to copy GridFunction data, use either Assign or + # numpy representation. + # u_tmp.Assign(u_gf) + # u_tmp.GetDataArray()[:] = u_gf.GetDataArray() + + gamma = 1.0 + delta_psi_gf *= gamma + psi_gf += delta_psi_gf + + if visualization: + sol_sock << "parallel " << num_procs << " " << myid << "\n" + sol_sock << "solution\n" << pmesh << u_gf + sol_sock << "window_title 'Discrete solution'" + sol_sock.flush() + + if myid == 0: + print("Newton_update_size = {:g}".format(Newton_update_size)) + + del A01 + + if Newton_update_size < increment_u: + break + + u_tmp.Assign(u_gf) + u_tmp -= u_old_gf + increment_u = u_tmp.ComputeL2Error(zero) + + if myid == 0: + print("Number of Newton iterations = " + str(j+1)) + print("Increment (|| uₕ - uₕ_prvs||) = " + + "{:g}".format(increment_u)) + + u_old_gf.Assign(u_gf) + psi_old_gf.Assign(psi_gf) + + if increment_u < tol or k == max_it-1: + break + + H1_error = u_gf.ComputeH1Error(exact_coef, exact_grad_coef) + if myid == 0: + print("H1-error (|| u - uₕᵏ||) = " + + "{:g}".format(H1_error)) + + if myid == 0: + print("Outer iterations: " + str(k+1)) + print(" Total iterations: " + str(total_iterations)) + print(" Total dofs: " + + str(H1fes.GlobalTrueVSize() + L2fes.GlobalTrueVSize())) + + # 11. Exact solution. + if visualization: + err_sock = mfem.socketstream("localhost", 19916) + err_sock.precision(8) + + error_gf = mfem.ParGridFunction(H1fes) + error_gf.ProjectCoefficient(exact_coef) + error_gf -= u_gf + + err_sock << "parallel " << num_procs << " " << myid << "\n" + err_sock << "solution\n" << pmesh << error_gf << "window_title 'Error'" + err_sock.flush() + + L2_error = u_gf.ComputeL2Error(exact_coef) + H1_error = u_gf.ComputeH1Error(exact_coef, exact_grad_coef) + + c_psi_gf = mfem.GridFunctionCoefficient(psi_gf) + + @mfem.jit.scalar(dependency=(c_psi_gf, obstacle)) + def u_alt_cf(ptx, val, obstacle): + min_val = 0 + max_val = 1e36 + return min(max_val, max(min_val, exp(val)+obstacle)) + + u_alt_gf = mfem.ParGridFunction(L2fes) + u_alt_gf.ProjectCoefficient(u_alt_cf) + L2_error_alt = u_alt_gf.ComputeL2Error(exact_coef) + + if myid == 0: + print("\n Final L2-error (|| u - uₕ||) = " + + "{:g}".format(L2_error)) + print(" Final H1-error (|| u - uₕ||) = " + + "{:g}".format(H1_error)) + print(" Final L2-error (|| u - ϕ - exp(ψₕ)||) = " + + "{:g}".format(L2_error_alt)) + + +@njit(float64(float64, float64)) +def spherical_obstacle(x, y): + r = sqrt(x*x + y*y) + r0 = 0.5 + beta = 0.9 + + b = r0*beta + tmp = sqrt(r0*r0 - b*b) + B = tmp + b*b/tmp + C = -b/tmp + + if r > b: + return B + r * C + else: + return sqrt(r0*r0 - r*r) + + +@njit(float64(float64, float64)) +def exact_solution_obstacle(x, y): + r = sqrt(x*x + y*y) + r0 = 0.5 + a = 0.348982574111686 + A = -0.340129705945858 + + if r > a: + return A * log(r) + else: + return sqrt(r0*r0-r*r) + + +@njit(float64[:](float64, float64)) +def exact_solution_gradient_obstacle(x, y): + r = sqrt(x*x + y*y) + r0 = 0.5 + a = 0.348982574111686 + A = -0.340129705945858 + + grad = np.zeros(2, dtype=np.float64) + if r > a: + grad[0] = A * x / (r*r) + grad[1] = A * y / (r*r) + else: + grad[0] = - x / sqrt(r0*r0 - r*r) + grad[1] = - y / sqrt(r0*r0 - r*r) + return grad + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser(description='Ex36p (Obstacle problem)') + + parser.add_argument("-o", "--order", + action='store', default=1, type=int, + help="Finite element order (polynomial degree).") + parser.add_argument('-r', '--refs', + action='store', default=3, type=int, + help="Number of times to refine the mesh uniformly.") + parser.add_argument('-mi', '--max-it', + action='store', default=10, type=int, + help="Maximum number of iterations") + help = "\n".join(("Stopping criteria based on the difference between", + "successive solution updates")) + parser.add_argument('-tol', '--tol', + action='store', default=1e-5, type=float, + help=help) + parser.add_argument('-step', '--step', + action='store', default=1.0, type=float, + help="Step size alpha") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + + args = parser.parse_args() + if myid == 0: + parser.print_options(args) + + globals()["visualization"] = not args.no_visualization + + run(refs=args.refs, + order=args.order, + max_it=args.max_it, + tol=args.tol, + alpha=args.step) diff --git a/examples/ex37.py b/examples/ex37.py new file mode 100644 index 00000000..7cc8090a --- /dev/null +++ b/examples/ex37.py @@ -0,0 +1,631 @@ +''' + PyMFEM example 37 + + See c++ version in the MFEM library for more detail + + Sample runs: + python ex37.py -alpha 10 + python ex37.py -alpha 10 -pv + python ex37.py -lambda 0.1 -mu 0.1 + python ex37.py -o 2 -alpha 5.0 -mi 50 -vf 0.4 -ntol 1e-5 + python ex37.py -r 6 -o 1 -alpha 25.0 -epsilon 0.02 -mi 50 -ntol 1e-5 + + + Description: This example code demonstrates the use of MFEM to solve a + density-filtered [3] topology optimization problem. The + objective is to minimize the compliance + + minimize ∫_Ω f⋅u dx over u ∈ [H¹(Ω)]² and ρ ∈ L¹(Ω) + + subject to + + -Div(r(ρ̃)Cε(u)) = f in Ω + BCs + -ϵ²Δρ̃ + ρ̃ = ρ in Ω + Neumann BCs + 0 ≤ ρ ≤ 1 in Ω + ∫_Ω ρ dx = θ vol(Ω) + + Here, r(ρ̃) = ρ₀ + ρ̃³ (1-ρ₀) is the solid isotropic material + penalization (SIMP) law, C is the elasticity tensor for an + isotropic linearly elastic material, ϵ > 0 is the design + length scale, and 0 < θ < 1 is the volume fraction. + + The problem is discretized and gradients are computing using + finite elements [1]. The design is optimized using an entropic + mirror descent algorithm introduced by Keith and Surowiec [2] + that is tailored to the bound constraint 0 ≤ ρ ≤ 1. + + This example highlights the ability of MFEM to deliver high- + order solutions to inverse design problems and showcases how + to set up and solve PDE-constrained optimization problems + using the so-called reduced space approach. + + [1] Andreassen, E., Clausen, A., Schevenels, M., Lazarov, B. S., & Sigmund, O. + (2011). Efficient topology optimization in MATLAB using 88 lines of + code. Structural and Multidisciplinary Optimization, 43(1), 1-16. + [2] Keith, B. and Surowiec, T. (2023) Proximal Galerkin: A structure- + preserving finite element method for pointwise bound constraints. + arXiv:2307.12444 [math.NA] + [3] Lazarov, B. S., & Sigmund, O. (2011). Filters in topology optimization + based on Helmholtz‐type differential equations. International Journal + for Numerical Methods in Engineering, 86(6), 765-781. + +''' +import mfem.ser as mfem +from mfem.ser import intArray, doubleArray + +from ex37_common import (sigmoid, + der_sigmoid, + inv_sigmoid, + MappedGridFunctionCoefficient, + DiffMappedGridFunctionCoefficient, + SIMPInterpolationCoefficient, + VolumeForceCoefficient, + ) +import os +from os.path import expanduser, join +import numpy as np +from numpy import sin, cos, array, pi, sqrt, floor + +visualization = True +paraview_output = False + + +class StrainEnergyDensityCoefficient(): + ''' + Python Note: + Approach here is to replace Eval and GetVectorGradient method call in C++ + using the dependency feature of mfem.jit. + + GetVectorGradient is mimiced by creating GradientGridFunctionCoefficient + for each component of u vector. Note GridFunction(fes, u.GetDataArray()) + reuses the data array from u. + ''' + + def __init__(self, llambda, mu, u, rho_filter, rho_min=1e-6, exponent=3.0): + assert rho_min >= 0.0, "rho_min must be >= 0" + assert rho_min < 1.0, "rho_min must be > 1" + + fes = u.FESpace() + assert fes.GetOrdering() == mfem.Ordering.byNODES, "u has to use byNODES ordering" + + mesh = fes.GetMesh() + dim = mesh.Dimension() + assert dim == 2, "dim must be two." + + fec = fes.FEColl() + fes = mfem.FiniteElementSpace(mesh, fec) + size = len(u.GetDataArray()) + + u1 = mfem.GridFunction(fes, mfem.Vector( + u.GetDataArray())) # first component + u2 = mfem.GridFunction(fes, mfem.Vector( + u.GetDataArray()), size//2) # second component + + c_gradu1 = mfem.GradientGridFunctionCoefficient(u1) + c_gradu2 = mfem.GradientGridFunctionCoefficient(u2) + + c_rho_filter = mfem.GridFunctionCoefficient(rho_filter) + + @mfem.jit.scalar(dependency=(llambda, mu, c_gradu1, c_gradu2, c_rho_filter)) + def coeff(ptx, L, M, grad1, grad2, val): + div_u = grad1[0] + grad2[1] + density = L*div_u*div_u + + grad = np.zeros(shape=(2, 2), dtype=np.float64) + grad[0, 0] = grad1[0] + grad[0, 1] = grad1[1] + grad[1, 0] = grad2[0] + grad[1, 1] = grad2[1] + + for i in range(2): + for j in range(2): + density += M*grad[i, j]*(grad[i, j] + grad[j, i]) + return -exponent * val**(exponent-1.0)*(1-rho_min)*density + + self.fes = fes + self.size = size + self.u1u2 = (u1, u2) + self.dependency = (c_gradu1, c_gradu2, c_rho_filter) + self.coeff = coeff + + def Update(self, u, rho_filter): + u1 = mfem.GridFunction(self.fes, mfem.Vector(u.GetDataArray())) + u2 = mfem.GridFunction(self.fes, mfem.Vector(u.GetDataArray()), + self.size//2) + self.dependency[0].SetGridFunction(u1) + self.dependency[1].SetGridFunction(u2) + self.dependency[2].SetGridFunction(rho_filter) + self.u1u2 = (u1, u2) + + +class DiffusionSolver(): + def __init__(self): + self.rhscf = None + self.neumann_cf = None + self.masscf = None + self.essbdr_cf = None + self.gradient_cf = None + + def SetupFEM(self): + dim = self.mesh.Dimension() + self.fec = mfem.H1_FECollection(self.order, dim) + self.fes = mfem.FiniteElementSpace(self.mesh, self.fec) + + if self.ess_bdr.Size() == 0 and self.mesh.bdr_attributes.Size() > 0: + self.ess_bdr = mfem.intArray([1]*self.mesh.bdr_attributes.Max()) + + def Solve(self): + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + ess_tdof_list = mfem.intArray() + self.fes.GetEssentialTrueDofs(self.ess_bdr, ess_tdof_list) + + self.u = mfem.GridFunction(self.fes) + self.u.Assign(0.0) + + b = mfem.LinearForm(self.fes) + + if self.rhscf is not None: + itg = mfem.DomainLFIntegrator(self.rhscf) + b.AddDomainIntegrator(itg) + + if self.neumann_cf is not None: + assert self.neumann_bdr.Size() > 0, "neumann_bdr attributes not provided" + b.AddBoundaryIntegrator(mfem.BoundaryLFIntegrator(self.neumann_cf), + self.neumann_bdr) + elif self.gradient_cf is not None: + assert self.neumann_bdr.Size() > 0, "neumann_bdr attributes not provided" + b.AddBoundaryIntegrator(mfem.BoundaryNormalLFIntegrator(self.gradient_cf), + self.neumann_bdr) + + b.Assemble() + + a = mfem.BilinearForm(self.fes) + a.AddDomainIntegrator(mfem.DiffusionIntegrator(self.diffcf)) + if self.masscf is not None: + a.AddDomainIntegrator(mfem.MassIntegrator(self.masscf)) + a.Assemble() + if self.essbdr_cf is not None: + self.u.ProjectBdrCoefficient(essbdr_cf, ess_bdr) + + a.FormLinearSystem(ess_tdof_list, self.u, b, A, X, B) + AA = A.AsSparseMatrix() + M = mfem.GSSmoother(AA) + cg = mfem.CGSolver() + cg.SetRelTol(1e-12) + cg.SetMaxIter(10000) + cg.SetPrintLevel(0) + cg.SetPreconditioner(M) + cg.SetOperator(A) + cg.Mult(B, X) + + a.RecoverFEMSolution(X, b, self.u) + self.b = b + + def GetFEMSolution(self): + return self.u + + def SetRHSCoefficient(self, rhscf): + self.rhscf = rhscf + + +class LinearElasticitySolver(): + def __init__(self): + self.rhs_cf = None + self.essbdr_cf = None + + def SetupFEM(self): + dim = self.mesh.Dimension() + self.fec = mfem.H1_FECollection( + self.order, dim, mfem.BasisType.Positive) + self.fes = mfem.FiniteElementSpace(self.mesh, self.fec, dim) + self.u = mfem.GridFunction(self.fes) + self.u.Assign(0.0) + + def Solve(self): + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + + ess_tdof_list = mfem.intArray() + self.fes.GetEssentialTrueDofs(self.ess_bdr, ess_tdof_list) + + x = mfem.GridFunction(self.fes) + x .Assign(0.0) + + self.u.Assign(0.0) + b = mfem.LinearForm(self.fes) + + if self.rhs_cf is not None: + b.AddDomainIntegrator(mfem.VectorDomainLFIntegrator(self.rhs_cf)) + b.Assemble() + + a = mfem.BilinearForm(self.fes) + a.AddDomainIntegrator( + mfem.ElasticityIntegrator(self.lambda_cf, self.mu_cf)) + a.Assemble() + if self.essbdr_cf is not None: + u.ProjectBdrCoefficient(self.essbdr_cf, self.ess_bdr) + + a.FormLinearSystem(ess_tdof_list, x, b, A, X, B) + + AA = A.AsSparseMatrix() + M = mfem.GSSmoother(AA) + cg = mfem.CGSolver() + + cg.SetRelTol(1e-10) + cg.SetMaxIter(10000) + cg.SetPrintLevel(0) + cg.SetPreconditioner(M) + cg.SetOperator(A) + cg.Mult(B, X) + a.RecoverFEMSolution(X, b, x) + + self.u += x + self.b = b + + def GetFEMSolution(self): + return self.u + + def GetLinearForm(self): + return self.b + + +class Proj(): + ''' + + @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace + ∫_Ω ρ dx = θ vol(Ω) as follows: + + 1. Compute the root of the R → R function + f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω) + 2. Set ψ ← ψ + c. + + @param psi a GridFunction to be updated + @param target_volume θ vol(Ω) + @param tol Newton iteration tolerance + @param max_its Newton maximum iteration number + @return double Final volume, ∫_Ω sigmoid(ψ) + + ''' + + def __init__(self, psi): + self.psi = psi + self.sigmoid_psi = MappedGridFunctionCoefficient(psi, sigmoid) + self.der_sigmoid_psi = MappedGridFunctionCoefficient(psi, der_sigmoid) + + def __call__(self, target_volume, tol=1e-12, max_its=10): + psi = self.psi + int_sigmoid_psi = mfem.LinearForm(psi.FESpace()) + int_sigmoid_psi.AddDomainIntegrator( + mfem.DomainLFIntegrator(self.sigmoid_psi)) + int_der_sigmoid_psi = mfem.LinearForm(psi.FESpace()) + int_der_sigmoid_psi.AddDomainIntegrator(mfem.DomainLFIntegrator( + self.der_sigmoid_psi)) + done = False + for k in range(max_its): # Newton iteration + int_sigmoid_psi.Assemble() # Recompute f(c) with updated ψ + f = int_sigmoid_psi.Sum() - target_volume + + int_der_sigmoid_psi.Assemble() # Recompute df(c) with updated ψ + df = int_der_sigmoid_psi.Sum() + + dc = -f/df + psi += dc + if abs(dc) < tol: + done = True + break + + if not done: + message = ("Projection reached maximum iteration without converging. " + + "Result may not be accurate.") + import warnigns + warnings.warn(message, RuntimeWarning) + + int_sigmoid_psi.Assemble() + return int_sigmoid_psi.Sum() + + +def run(ref_levels=5, + order=2, + alpha=1.0, + epsilon=0.01, + vol_fraction=0.5, + max_it=1e3, + itol=1e-1, + ntol=1e-4, + rho_min=1e-6, + llambda=1.0, + mu=1.0,): + + mesh = mfem.Mesh.MakeCartesian2D(3, 1, mfem.Element.QUADRILATERAL, + True, 3.0, 1.0) + dim = mesh.Dimension() + + # 2. Set BCs. + for i in range(mesh.GetNBE()): + be = mesh.GetBdrElement(i) + vertices = mesh.GetBdrElementVertices(i) # this method returns list + + coords1 = mesh.GetVertexArray(vertices[0]) # this returns numpy array + coords2 = mesh.GetVertexArray(vertices[1]) + + center = (coords1 + coords2)/2 + + if abs(center[0] - 0.0) < 1e-10: + # the left edge + be.SetAttribute(1) + else: + # all other boundaries + be.SetAttribute(2) + mesh.SetAttributes() + + # 3. Refine the mesh. + for lev in range(ref_levels): + mesh.UniformRefinement() + + # 4. Define the necessary finite element spaces on the mesh. + state_fec = mfem.H1_FECollection(order, dim) # space for u + filter_fec = mfem.H1_FECollection(order, dim) # space for ρ̃ + control_fec = mfem.L2_FECollection(order-1, dim, + mfem.BasisType.GaussLobatto) # space for ψ + state_fes = mfem.FiniteElementSpace(mesh, state_fec, dim) + filter_fes = mfem.FiniteElementSpace(mesh, filter_fec) + control_fes = mfem.FiniteElementSpace(mesh, control_fec) + + state_size = state_fes.GetTrueVSize() + control_size = control_fes.GetTrueVSize() + filter_size = filter_fes.GetTrueVSize() + + print("Number of state unknowns: " + str(state_size)) + print("Number of filter unknowns: " + str(filter_size)) + print("Number of control unknowns: " + str(control_size)) + + # 5. Set the initial guess for ρ. + u = mfem.GridFunction(state_fes) + psi = mfem.GridFunction(control_fes) + psi_old = mfem.GridFunction(control_fes) + rho_filter = mfem.GridFunction(filter_fes) + + u.Assign(0.0) + rho_filter.Assign(vol_fraction) + psi.Assign(inv_sigmoid(vol_fraction)) + psi_old.Assign(inv_sigmoid(vol_fraction)) + + # ρ = sigmoid(ψ) + rho = MappedGridFunctionCoefficient(psi, sigmoid) + # Interpolation of ρ = sigmoid(ψ) in control fes (for ParaView output) + rho_gf = mfem.GridFunction(control_fes) + # ρ - ρ_old = sigmoid(ψ) - sigmoid(ψ_old) + succ_diff_rho = DiffMappedGridFunctionCoefficient(psi, psi_old, sigmoid) + + # 6. Set-up the physics solver. + maxat = mesh.bdr_attributes.Max() + ess_bdr = intArray([0]*maxat) + ess_bdr[0] = 1 + + one = mfem.ConstantCoefficient(1.0) + lambda_cf = mfem.ConstantCoefficient(llambda) + mu_cf = mfem.ConstantCoefficient(mu) + + ElasticitySolver = LinearElasticitySolver() + ElasticitySolver.mesh = mesh + ElasticitySolver.order = state_fec.GetOrder() + ElasticitySolver.SetupFEM() + + center = np.array((2.9, 0.5)) + force = np.array((0.0, -1.0)) + r = 0.05 + vforce_cf = VolumeForceCoefficient(r, center, force) + ElasticitySolver.rhs_cf = vforce_cf + ElasticitySolver.ess_bdr = ess_bdr + + # 7. Set-up the filter solver. + eps2_cf = mfem.ConstantCoefficient(epsilon*epsilon) + FilterSolver = DiffusionSolver() + FilterSolver.mesh = mesh + FilterSolver.order = filter_fec.GetOrder() + FilterSolver.diffcf = eps2_cf + FilterSolver.masscf = one + + if mesh.bdr_attributes.Size() > 0: + ess_bdr_filter = mfem.intArray([0]*mesh.bdr_attributes.Max()) + else: + ess_bdr_filter = mfem.intArray() + + FilterSolver.ess_bdr = ess_bdr_filter + FilterSolver.SetupFEM() + + mass = mfem.BilinearForm(control_fes) + mass.AddDomainIntegrator(mfem.InverseIntegrator(mfem.MassIntegrator(one))) + mass.Assemble() + M = mfem.SparseMatrix() + empty = mfem.intArray() + mass.FormSystemMatrix(empty, M) + + # 8. Define the Lagrange multiplier and gradient functions. + grad = mfem.GridFunction(control_fes) + w_filter = mfem.GridFunction(filter_fes) + + # 9. Define some tools for later. + zero = mfem.ConstantCoefficient(0.0) + onegf = mfem.GridFunction(control_fes) + onegf.Assign(1.0) + zerogf = mfem.GridFunction(control_fes) + zerogf.Assign(0.0) + + vol_form = mfem.LinearForm(control_fes) + vol_form.AddDomainIntegrator(mfem.DomainLFIntegrator(one)) + vol_form.Assemble() + domain_volume = vol_form(onegf) + target_volume = domain_volume * vol_fraction + + # 10. Connect to GLVis. Prepare for VisIt output. + if visualization: + sout_r = mfem.socketstream("localhost", 19916) + sout_r.precision(8) + + if paraview_output: + paraview_dc = mfem.ParaViewDataCollection("ex37", mesh) + + rho_gf.ProjectCoefficient(rho) + paraview_dc.SetPrefixPath("ParaView") + paraview_dc.SetLevelsOfDetail(order) + paraview_dc.SetDataFormat(mfem.VTKFormat.BINARY) + paraview_dc.SetHighOrderOutput(True) + paraview_dc.SetCycle(0) + paraview_dc.SetTime(0.0) + paraview_dc.RegisterField("displacement", u) + paraview_dc.RegisterField("density", rho_gf) + paraview_dc.RegisterField("filtered_density", rho_filter) + paraview_dc.Save() + + # 11. Iterate: + proj = Proj(psi) + #max_it = 1 + for k in range(1, max_it+1): + if k > 1: + alpha *= k/(k-1.) + + print("\nStep = " + str(k)) + + # Step 1 - Filter solve + # Solve (ϵ^2 ∇ ρ̃, ∇ v ) + (ρ̃,v) = (ρ,v) + FilterSolver.SetRHSCoefficient(rho) + FilterSolver.Solve() + rho_filter = FilterSolver.GetFEMSolution() + + # Step 2 - State solve + # Solve (λ r(ρ̃) ∇⋅u, ∇⋅v) + (2 μ r(ρ̃) ε(u), ε(v)) = (f,v) + if k == 1: + SIMP = SIMPInterpolationCoefficient(rho_filter, rho_min, 1.0) + SIMP_cf = SIMP.coeff + else: + SIMP.Update(rho_filter) + + lambda_SIMP_cf = mfem.ProductCoefficient(lambda_cf, SIMP_cf) + mu_SIMP_cf = mfem.ProductCoefficient(mu_cf, SIMP_cf) + + ElasticitySolver.lambda_cf = lambda_SIMP_cf + ElasticitySolver.mu_cf = mu_SIMP_cf + + ElasticitySolver.Solve() + u = ElasticitySolver.GetFEMSolution() + + # Step 3 - Adjoint filter solve + # Solve (ϵ² ∇ w̃, ∇ v) + (w̃ ,v) = (-r'(ρ̃) ( λ |∇⋅u|² + 2 μ |ε(u)|²),v) + if k == 1: + SEDC = StrainEnergyDensityCoefficient(lambda_cf, mu_cf, u, rho_filter, + rho_min) + rhs_cf = SEDC.coeff + else: + SEDC.Update(u, rho_filter) + + FilterSolver.SetRHSCoefficient(rhs_cf) + FilterSolver.Solve() + w_filter = FilterSolver.GetFEMSolution() + + # Step 4 - Compute gradient + # Solve G = M⁻¹w̃ + w_cf = mfem.GridFunctionCoefficient(w_filter) + w_rhs = mfem.LinearForm(control_fes) + w_rhs.AddDomainIntegrator(mfem.DomainLFIntegrator(w_cf)) + w_rhs.Assemble() + M.Mult(w_rhs, grad) + + # Step 5 - Update design variable ψ ← proj(ψ - αG) + psi.Add(-alpha, grad) + material_volume = proj(target_volume) + + # Compute ||ρ - ρ_old|| in control fes. + norm_increment = zerogf.ComputeL1Error(succ_diff_rho) + norm_reduced_gradient = norm_increment/alpha + psi_old.Assign(psi) + + compliance = (ElasticitySolver.GetLinearForm())(u) + print("norm of the reduced gradient = " + + "{:g}".format(norm_reduced_gradient)) + print("norm of the increment = " + "{:g}".format(norm_increment)) + print("compliance = " + "{:g}".format(compliance)) + print("volume fraction = " + + "{:g}".format(material_volume / domain_volume)) + + if visualization: + r_gf = mfem.GridFunction(filter_fes) + r_gf.ProjectCoefficient(SIMP_cf) + sout_r << "solution\n" << mesh << r_gf << "window_title 'Design density r(ρ̃)'" + sout_r.flush() + + if paraview_output: + rho_gf.ProjectCoefficient(rho) + paraview_dc.SetCycle(k) + paraview_dc.SetTime(float(k)) + paraview_dc.Save() + + if norm_reduced_gradient < ntol and norm_increment < itol: + break + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser(description='Ex37 (Topology Optimization)') + + parser.add_argument('-r', '--ref_levels', + action='store', default=5, type=int, + help="Number of times to refine the mesh uniformly.") + parser.add_argument("-o", "--order", + action='store', default=2, type=int, + help="Order (degree) of the finite elements.") + parser.add_argument("-alpha", "--alpha-step-length", + action='store', default=1.0, type=float, + help="Step length for gradient descent.") + parser.add_argument("-epsilon", "--epsilon-thickness", + action='store', default=0.01, type=float, + help="Length scale for ρ.") + parser.add_argument("-mi", "--max-it", + action='store', default=1000, type=int, + help="Maximum number of gradient descent iterations.") + parser.add_argument("-ntol", "--rel-tol", + action='store', default=1e-4, type=float, + help="Normalized exit tolerance.") + parser.add_argument("-itol", "--abs-tol", + action='store', default=1e-1, type=float, + help="Increment exit tolerance.") + parser.add_argument("-vf", "--volume-fraction", + action='store', default=0.5, type=float, + help="Volume fraction for the material density.") + parser.add_argument("-lambda", "--llambda", + action='store', default=1.0, type=float, + help="Lamé constant λ.") + parser.add_argument("-mu", "--mu", + action='store', default=1.0, type=float, + help="Lamé constant μ.") + parser.add_argument("-rmin", "--psi-min", + action='store', default=1e-6, type=float, + help="Minimum of density coefficient.") + parser.add_argument("-pv", "--paraview", + action='store_true', default=False, + help="Enable or disable ParaView output.") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + + args = parser.parse_args() + parser.print_options(args) + + globals()["visualization"] = not args.no_visualization + globals()["paraview_output"] = args.paraview + + run(ref_levels=args.ref_levels, + order=args.order, + alpha=args.alpha_step_length, + epsilon=args.epsilon_thickness, + vol_fraction=args.volume_fraction, + max_it=args.max_it, + itol=args.abs_tol, + ntol=args.rel_tol, + rho_min=args.psi_min, + llambda=args.llambda, + mu=args.mu) diff --git a/examples/ex37_common.py b/examples/ex37_common.py new file mode 100644 index 00000000..ec53373f --- /dev/null +++ b/examples/ex37_common.py @@ -0,0 +1,110 @@ +''' + PyMFEM example 37 - Serial/Parallel Shared code +''' + +import os +from os.path import expanduser, join + +from numpy import sqrt, log, exp +import numpy as np +from numba import njit +from numba.types import float64 + +from mfem import mfem_mode + +if mfem_mode == 'serial': + import mfem.ser as mfem + from mfem.ser import intArray, doubleArray + use_parallel = False +else: + import mfem.par as mfem + from mfem.par import intArray, doubleArray + use_parallel = True + + +@njit(float64(float64)) +def inv_sigmoid(x): + ''' + Inverse sigmoid function + ''' + tol = 1e-12 + x = min(max(tol, x), 1.0-tol) + return log(x/(1.0-x)) + + +@njit(float64(float64)) +def sigmoid(x): + ''' + Sigmoid function + ''' + if x >= 0: + return 1.0/(1.0 + exp(-x)) + else: + return exp(x)/(1.0 + exp(x)) + + +@njit(float64(float64)) +def der_sigmoid(x): + ''' + Derivative of sigmoid function + ''' + tmp = sigmoid(-x) + return tmp - tmp**2 + + +def MappedGridFunctionCoefficient(gf, func): + + c_gf = mfem.GridFunctionCoefficient(gf) + + @mfem.jit.scalar(dependency=(c_gf,)) + def coeff(ptx, c_gf): + return func(c_gf) + return coeff + + +def DiffMappedGridFunctionCoefficient(gf, other_gf, func, comp=1): + c_gf = mfem.GridFunctionCoefficient(gf) + c_ogf = mfem.GridFunctionCoefficient(other_gf) + + @mfem.jit.scalar(dependency=(c_gf, c_ogf)) + def coeff(ptx, c_gf, c_ogf): + return func(c_gf) - func(c_ogf) + return coeff + + +class SIMPInterpolationCoefficient(): + ''' + Python Note: + Approach here is to replace Eval in C++ example using the dependency + feature of mfem.jit. + + In order to avoid repeating Numba-Jitting in iteration loop, we use + SetGridFunction to update the GridFunction referred from + GridFunctionCoefficient. + ''' + + def __init__(self, rho_filter, min_val=1e-6, max_val=1.0, exponent=3): + val = mfem.GridFunctionCoefficient(rho_filter) + + @mfem.jit.scalar(dependency=(val,)) + def coeff(ptx, val): + coeff = min_val + val**exponent*(max_val-min_val) + return coeff + + self.c_gf = val + self.coeff = coeff + + def Update(self, rho_filter): + self.c_gf.SetGridFunction(rho_filter) + + +def VolumeForceCoefficient(r, center, force): + + @mfem.jit.vector(shape=(len(center),)) + def coeff(ptx): + cr = sqrt(sum((ptx - center)**2)) + if cr < r: + return np.array((force[0], force[1])) + else: + return np.array((0.0, 0.0)) + return coeff diff --git a/examples/ex37p.py b/examples/ex37p.py new file mode 100644 index 00000000..c9469200 --- /dev/null +++ b/examples/ex37p.py @@ -0,0 +1,650 @@ +''' + PyMFEM example 37 + + See c++ version in the MFEM library for more detail + + Sample runs: + python ex37.py -alpha 10 + python ex37.py -alpha 10 -pv + python ex37.py -lambda 0.1 -mu 0.1 + python ex37.py -o 2 -alpha 5.0 -mi 50 -vf 0.4 -ntol 1e-5 + python ex37.py -r 6 -o 1 -alpha 25.0 -epsilon 0.02 -mi 50 -ntol 1e-5 + + + Description: This example code demonstrates the use of MFEM to solve a + density-filtered [3] topology optimization problem. The + objective is to minimize the compliance + + minimize ∫_Ω f⋅u dx over u ∈ [H¹(Ω)]² and ρ ∈ L¹(Ω) + + subject to + + -Div(r(ρ̃)Cε(u)) = f in Ω + BCs + -ϵ²Δρ̃ + ρ̃ = ρ in Ω + Neumann BCs + 0 ≤ ρ ≤ 1 in Ω + ∫_Ω ρ dx = θ vol(Ω) + + Here, r(ρ̃) = ρ₀ + ρ̃³ (1-ρ₀) is the solid isotropic material + penalization (SIMP) law, C is the elasticity tensor for an + isotropic linearly elastic material, ϵ > 0 is the design + length scale, and 0 < θ < 1 is the volume fraction. + + The problem is discretized and gradients are computing using + finite elements [1]. The design is optimized using an entropic + mirror descent algorithm introduced by Keith and Surowiec [2] + that is tailored to the bound constraint 0 ≤ ρ ≤ 1. + + This example highlights the ability of MFEM to deliver high- + order solutions to inverse design problems and showcases how + to set up and solve PDE-constrained optimization problems + using the so-called reduced space approach. + + [1] Andreassen, E., Clausen, A., Schevenels, M., Lazarov, B. S., & Sigmund, O. + (2011). Efficient topology optimization in MATLAB using 88 lines of + code. Structural and Multidisciplinary Optimization, 43(1), 1-16. + [2] Keith, B. and Surowiec, T. (2023) Proximal Galerkin: A structure- + preserving finite element method for pointwise bound constraints. + arXiv:2307.12444 [math.NA] + [3] Lazarov, B. S., & Sigmund, O. (2011). Filters in topology optimization + based on Helmholtz‐type differential equations. International Journal + for Numerical Methods in Engineering, 86(6), 765-781. + +''' +import mfem.par as mfem +from mfem.par import intArray, doubleArray + +from ex37_common import (sigmoid, + der_sigmoid, + inv_sigmoid, + MappedGridFunctionCoefficient, + DiffMappedGridFunctionCoefficient, + SIMPInterpolationCoefficient, + VolumeForceCoefficient, + ) +import os +from os.path import expanduser, join +import numpy as np +from numpy import sin, cos, array, pi, sqrt, floor +from mpi4py import MPI + +num_procs = MPI.COMM_WORLD.size +myid = MPI.COMM_WORLD.rank +smyid = '{:0>6d}'.format(myid) + +visualization = True +paraview_output = False + + +class StrainEnergyDensityCoefficient(): + ''' + Python Note: + Approach here is to replace Eval and GetVectorGradient method call in C++ + using the dependency feature of mfem.jit. + + GetVectorGradient is mimiced by creating GradientGridFunctionCoefficient + for each component of u vector. Note GridFunction(fes, u.GetDataArray()) + reuses the data array from u. + ''' + + def __init__(self, llambda, mu, u, rho_filter, rho_min=1e-6, exponent=3.0): + assert rho_min >= 0.0, "rho_min must be >= 0" + assert rho_min < 1.0, "rho_min must be > 1" + + pfes = u.ParFESpace() + assert pfes.GetOrdering() == mfem.Ordering.byNODES, "u has to use byNODES ordering" + + pmesh = pfes.GetParMesh() + dim = pmesh.Dimension() + assert dim == 2, "dim must be two." + + fec = pfes.FEColl() + pfes = mfem.ParFiniteElementSpace(pmesh, fec) + size = len(u.GetDataArray()) + + u1 = mfem.ParGridFunction(pfes, mfem.Vector( + u.GetDataArray())) # first component + u2 = mfem.ParGridFunction(pfes, mfem.Vector( + u.GetDataArray()), size//2) # second component + + c_gradu1 = mfem.GradientGridFunctionCoefficient(u1) + c_gradu2 = mfem.GradientGridFunctionCoefficient(u2) + + c_rho_filter = mfem.GridFunctionCoefficient(rho_filter) + + @mfem.jit.scalar(dependency=(llambda, mu, c_gradu1, c_gradu2, c_rho_filter)) + def coeff(ptx, L, M, grad1, grad2, val): + div_u = grad1[0] + grad2[1] + density = L*div_u*div_u + + grad = np.zeros(shape=(2, 2), dtype=np.float64) + grad[0, 0] = grad1[0] + grad[0, 1] = grad1[1] + grad[1, 0] = grad2[0] + grad[1, 1] = grad2[1] + + for i in range(2): + for j in range(2): + density += M*grad[i, j]*(grad[i, j] + grad[j, i]) + return -exponent * val**(exponent-1.0)*(1-rho_min)*density + + self.pfes = pfes + self.size = size + self.u1u2 = (u1, u2) + self.dependency = (c_gradu1, c_gradu2, c_rho_filter) + self.coeff = coeff + + def Update(self, u, rho_filter): + u1 = mfem.ParGridFunction(self.pfes, mfem.Vector(u.GetDataArray())) + u2 = mfem.ParGridFunction(self.pfes, mfem.Vector(u.GetDataArray()), + self.size//2) + self.dependency[0].SetGridFunction(u1) + self.dependency[1].SetGridFunction(u2) + self.dependency[2].SetGridFunction(rho_filter) + self.u1u2 = (u1, u2) + + +class DiffusionSolver(): + def __init__(self): + self.rhscf = None + self.neumann_cf = None + self.masscf = None + self.essbdr_cf = None + self.gradient_cf = None + + def SetupFEM(self): + dim = self.pmesh.Dimension() + self.fec = mfem.H1_FECollection(self.order, dim) + self.pfes = mfem.ParFiniteElementSpace(self.pmesh, self.fec) + + if self.ess_bdr.Size() == 0 and self.pmesh.bdr_attributes.Size() > 0: + self.ess_bdr = mfem.intArray([1]*self.pmesh.bdr_attributes.Max()) + + def Solve(self): + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + ess_tdof_list = mfem.intArray() + self.pfes.GetEssentialTrueDofs(self.ess_bdr, ess_tdof_list) + + self.u = mfem.ParGridFunction(self.pfes) + self.u.Assign(0.0) + + b = mfem.ParLinearForm(self.pfes) + + if self.rhscf is not None: + itg = mfem.DomainLFIntegrator(self.rhscf) + b.AddDomainIntegrator(itg) + + if self.neumann_cf is not None: + assert self.neumann_bdr.Size() > 0, "neumann_bdr attributes not provided" + b.AddBoundaryIntegrator(mfem.BoundaryLFIntegrator(self.neumann_cf), + self.neumann_bdr) + elif self.gradient_cf is not None: + assert self.neumann_bdr.Size() > 0, "neumann_bdr attributes not provided" + b.AddBoundaryIntegrator(mfem.BoundaryNormalLFIntegrator(self.gradient_cf), + self.neumann_bdr) + + b.Assemble() + + a = mfem.ParBilinearForm(self.pfes) + a.AddDomainIntegrator(mfem.DiffusionIntegrator(self.diffcf)) + if self.masscf is not None: + a.AddDomainIntegrator(mfem.MassIntegrator(self.masscf)) + a.Assemble() + if self.essbdr_cf is not None: + self.u.ProjectBdrCoefficient(essbdr_cf, ess_bdr) + + a.FormLinearSystem(ess_tdof_list, self.u, b, A, X, B) + + M = mfem.HypreBoomerAMG() + M.SetPrintLevel(0) + cg = mfem.CGSolver(MPI.COMM_WORLD) + cg.SetRelTol(1e-12) + cg.SetMaxIter(10000) + cg.SetPrintLevel(0) + cg.SetPreconditioner(M) + cg.SetOperator(A.Ptr()) + cg.Mult(B, X) + + a.RecoverFEMSolution(X, b, self.u) + self.b = b + + def GetFEMSolution(self): + return self.u + + def SetRHSCoefficient(self, rhscf): + self.rhscf = rhscf + + +class LinearElasticitySolver(): + def __init__(self): + self.rhs_cf = None + self.essbdr_cf = None + + def SetupFEM(self): + dim = self.pmesh.Dimension() + self.fec = mfem.H1_FECollection( + self.order, dim, mfem.BasisType.Positive) + self.pfes = mfem.ParFiniteElementSpace(self.pmesh, self.fec, dim) + self.u = mfem.ParGridFunction(self.pfes) + self.u.Assign(0.0) + + def Solve(self): + A = mfem.OperatorPtr() + B = mfem.Vector() + X = mfem.Vector() + + ess_tdof_list = mfem.intArray() + self.pfes.GetEssentialTrueDofs(self.ess_bdr, ess_tdof_list) + + x = mfem.ParGridFunction(self.pfes) + x .Assign(0.0) + + self.u.Assign(0.0) + b = mfem.ParLinearForm(self.pfes) + + if self.rhs_cf is not None: + b.AddDomainIntegrator(mfem.VectorDomainLFIntegrator(self.rhs_cf)) + b.Assemble() + + a = mfem.ParBilinearForm(self.pfes) + a.AddDomainIntegrator( + mfem.ElasticityIntegrator(self.lambda_cf, self.mu_cf)) + a.Assemble() + if self.essbdr_cf is not None: + u.ProjectBdrCoefficient(self.essbdr_cf, self.ess_bdr) + + a.FormLinearSystem(ess_tdof_list, x, b, A, X, B) + + M = mfem.HypreBoomerAMG() + M.SetPrintLevel(0) + cg = mfem.CGSolver(MPI.COMM_WORLD) + + cg.SetRelTol(1e-10) + cg.SetMaxIter(10000) + cg.SetPrintLevel(0) + cg.SetPreconditioner(M) + cg.SetOperator(A.Ptr()) + cg.Mult(B, X) + a.RecoverFEMSolution(X, b, x) + + self.u += x + self.b = b + + def GetFEMSolution(self): + return self.u + + def GetParLinearForm(self): + return self.b + + +class Proj(): + ''' + + @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace + ∫_Ω ρ dx = θ vol(Ω) as follows: + + 1. Compute the root of the R → R function + f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω) + 2. Set ψ ← ψ + c. + + @param psi a GridFunction to be updated + @param target_volume θ vol(Ω) + @param tol Newton iteration tolerance + @param max_its Newton maximum iteration number + @return double Final volume, ∫_Ω sigmoid(ψ) + + ''' + + def __init__(self, psi): + self.psi = psi + self.sigmoid_psi = MappedGridFunctionCoefficient(psi, sigmoid) + self.der_sigmoid_psi = MappedGridFunctionCoefficient(psi, der_sigmoid) + + def __call__(self, target_volume, tol=1e-12, max_its=10): + psi = self.psi + int_sigmoid_psi = mfem.ParLinearForm(psi.ParFESpace()) + int_sigmoid_psi.AddDomainIntegrator( + mfem.DomainLFIntegrator(self.sigmoid_psi)) + int_der_sigmoid_psi = mfem.ParLinearForm(psi.ParFESpace()) + int_der_sigmoid_psi.AddDomainIntegrator(mfem.DomainLFIntegrator( + self.der_sigmoid_psi)) + done = False + for k in range(max_its): # Newton iteration + int_sigmoid_psi.Assemble() # Recompute f(c) with updated ψ + f = int_sigmoid_psi.Sum() + f = MPI.COMM_WORLD.allreduce(f, MPI.SUM) + f -= target_volume + + int_der_sigmoid_psi.Assemble() # Recompute df(c) with updated ψ + df = int_der_sigmoid_psi.Sum() + df = MPI.COMM_WORLD.allreduce(df, MPI.SUM) + dc = -f/df + psi += dc + if abs(dc) < tol: + done = True + break + + if not done: + message = ("Projection reached maximum iteration without converging. " + + "Result may not be accurate.") + import warnigns + warnings.warn(message, RuntimeWarning) + + int_sigmoid_psi.Assemble() + material_volume = int_sigmoid_psi.Sum() + material_volume = MPI.COMM_WORLD.allreduce(material_volume, MPI.SUM) + return material_volume + + +def run(ref_levels=5, + order=2, + alpha=1.0, + epsilon=0.01, + vol_fraction=0.5, + max_it=1e3, + itol=1e-1, + ntol=1e-4, + rho_min=1e-6, + llambda=1.0, + mu=1.0,): + + mesh = mfem.Mesh.MakeCartesian2D(3, 1, mfem.Element.QUADRILATERAL, + True, 3.0, 1.0) + dim = mesh.Dimension() + + # 2. Set BCs. + for i in range(mesh.GetNBE()): + be = mesh.GetBdrElement(i) + vertices = mesh.GetBdrElementVertices(i) # this method returns list + + coords1 = mesh.GetVertexArray(vertices[0]) # this returns numpy array + coords2 = mesh.GetVertexArray(vertices[1]) + + center = (coords1 + coords2)/2 + + if abs(center[0] - 0.0) < 1e-10: + # the left edge + be.SetAttribute(1) + else: + # all other boundaries + be.SetAttribute(2) + mesh.SetAttributes() + + # 3. Refine the mesh. + for lev in range(ref_levels): + mesh.UniformRefinement() + pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) + mesh.Clear() + + # 4. Define the necessary finite element spaces on the mesh. + state_fec = mfem.H1_FECollection(order, dim) # space for u + filter_fec = mfem.H1_FECollection(order, dim) # space for ρ̃ + control_fec = mfem.L2_FECollection(order-1, dim, + mfem.BasisType.GaussLobatto) # space for ψ + state_fes = mfem.ParFiniteElementSpace(pmesh, state_fec, dim) + filter_fes = mfem.ParFiniteElementSpace(pmesh, filter_fec) + control_fes = mfem.ParFiniteElementSpace(pmesh, control_fec) + + state_size = state_fes.GlobalTrueVSize() + control_size = control_fes.GlobalTrueVSize() + filter_size = filter_fes.GlobalTrueVSize() + + if myid == 0: + print("Number of state unknowns: " + str(state_size)) + print("Number of filter unknowns: " + str(filter_size)) + print("Number of control unknowns: " + str(control_size)) + + # 5. Set the initial guess for ρ. + u = mfem.ParGridFunction(state_fes) + psi = mfem.ParGridFunction(control_fes) + psi_old = mfem.ParGridFunction(control_fes) + rho_filter = mfem.ParGridFunction(filter_fes) + + u.Assign(0.0) + rho_filter.Assign(vol_fraction) + psi.Assign(inv_sigmoid(vol_fraction)) + psi_old.Assign(inv_sigmoid(vol_fraction)) + + # ρ = sigmoid(ψ) + rho = MappedGridFunctionCoefficient(psi, sigmoid) + # Interpolation of ρ = sigmoid(ψ) in control fes (for ParaView output) + rho_gf = mfem.ParGridFunction(control_fes) + # ρ - ρ_old = sigmoid(ψ) - sigmoid(ψ_old) + succ_diff_rho = DiffMappedGridFunctionCoefficient(psi, psi_old, sigmoid) + + # 6. Set-up the physics solver. + maxat = pmesh.bdr_attributes.Max() + ess_bdr = intArray([0]*maxat) + ess_bdr[0] = 1 + + one = mfem.ConstantCoefficient(1.0) + lambda_cf = mfem.ConstantCoefficient(llambda) + mu_cf = mfem.ConstantCoefficient(mu) + + ElasticitySolver = LinearElasticitySolver() + ElasticitySolver.pmesh = pmesh + ElasticitySolver.order = state_fec.GetOrder() + ElasticitySolver.SetupFEM() + + center = np.array((2.9, 0.5)) + force = np.array((0.0, -1.0)) + r = 0.05 + vforce_cf = VolumeForceCoefficient(r, center, force) + ElasticitySolver.rhs_cf = vforce_cf + ElasticitySolver.ess_bdr = ess_bdr + + # 7. Set-up the filter solver. + eps2_cf = mfem.ConstantCoefficient(epsilon*epsilon) + FilterSolver = DiffusionSolver() + FilterSolver.pmesh = pmesh + FilterSolver.order = filter_fec.GetOrder() + FilterSolver.diffcf = eps2_cf + FilterSolver.masscf = one + + if pmesh.bdr_attributes.Size() > 0: + ess_bdr_filter = mfem.intArray([0]*pmesh.bdr_attributes.Max()) + else: + ess_bdr_filter = mfem.intArray() + + FilterSolver.ess_bdr = ess_bdr_filter + FilterSolver.SetupFEM() + + mass = mfem.ParBilinearForm(control_fes) + mass.AddDomainIntegrator(mfem.InverseIntegrator(mfem.MassIntegrator(one))) + mass.Assemble() + M = mfem.HypreParMatrix() + empty = mfem.intArray() + mass.FormSystemMatrix(empty, M) + + # 8. Define the Lagrange multiplier and gradient functions. + grad = mfem.ParGridFunction(control_fes) + w_filter = mfem.ParGridFunction(filter_fes) + + # 9. Define some tools for later. + zero = mfem.ConstantCoefficient(0.0) + onegf = mfem.ParGridFunction(control_fes) + onegf.Assign(1.0) + zerogf = mfem.ParGridFunction(control_fes) + zerogf.Assign(0.0) + + vol_form = mfem.ParLinearForm(control_fes) + vol_form.AddDomainIntegrator(mfem.DomainLFIntegrator(one)) + vol_form.Assemble() + domain_volume = vol_form(onegf) + target_volume = domain_volume * vol_fraction + + # 10. Connect to GLVis. Prepare for VisIt output. + if visualization: + sout_r = mfem.socketstream("localhost", 19916) + sout_r.precision(8) + + if paraview_output: + paraview_dc = mfem.ParaViewDataCollection("ex37p", pmesh) + + rho_gf.ProjectCoefficient(rho) + paraview_dc.SetPrefixPath("ParaView") + paraview_dc.SetLevelsOfDetail(order) + paraview_dc.SetDataFormat(mfem.VTKFormat.BINARY) + paraview_dc.SetHighOrderOutput(True) + paraview_dc.SetCycle(0) + paraview_dc.SetTime(0.0) + paraview_dc.RegisterField("displacement", u) + paraview_dc.RegisterField("density", rho_gf) + paraview_dc.RegisterField("filtered_density", rho_filter) + paraview_dc.Save() + + # 11. Iterate: + proj = Proj(psi) + for k in range(1, max_it+1): + if k > 1: + alpha *= k/(k-1.) + + if myid == 0: + print("\nStep = " + str(k)) + + # Step 1 - Filter solve + # Solve (ϵ^2 ∇ ρ̃, ∇ v ) + (ρ̃,v) = (ρ,v) + FilterSolver.SetRHSCoefficient(rho) + FilterSolver.Solve() + rho_filter = FilterSolver.GetFEMSolution() + + # Step 2 - State solve + # Solve (λ r(ρ̃) ∇⋅u, ∇⋅v) + (2 μ r(ρ̃) ε(u), ε(v)) = (f,v) + if k == 1: + SIMP = SIMPInterpolationCoefficient(rho_filter, rho_min, 1.0) + SIMP_cf = SIMP.coeff + else: + SIMP.Update(rho_filter) + + lambda_SIMP_cf = mfem.ProductCoefficient(lambda_cf, SIMP_cf) + mu_SIMP_cf = mfem.ProductCoefficient(mu_cf, SIMP_cf) + + ElasticitySolver.lambda_cf = lambda_SIMP_cf + ElasticitySolver.mu_cf = mu_SIMP_cf + + ElasticitySolver.Solve() + u = ElasticitySolver.GetFEMSolution() + + # Step 3 - Adjoint filter solve + # Solve (ϵ² ∇ w̃, ∇ v) + (w̃ ,v) = (-r'(ρ̃) ( λ |∇⋅u|² + 2 μ |ε(u)|²),v) + if k == 1: + SEDC = StrainEnergyDensityCoefficient(lambda_cf, mu_cf, u, rho_filter, + rho_min) + rhs_cf = SEDC.coeff + else: + SEDC.Update(u, rho_filter) + + FilterSolver.SetRHSCoefficient(rhs_cf) + FilterSolver.Solve() + w_filter = FilterSolver.GetFEMSolution() + + # Step 4 - Compute gradient + # Solve G = M⁻¹w̃ + w_cf = mfem.GridFunctionCoefficient(w_filter) + w_rhs = mfem.ParLinearForm(control_fes) + w_rhs.AddDomainIntegrator(mfem.DomainLFIntegrator(w_cf)) + w_rhs.Assemble() + M.Mult(w_rhs, grad) + + # Step 5 - Update design variable ψ ← proj(ψ - αG) + psi.Add(-alpha, grad) + material_volume = proj(target_volume) + + # Compute ||ρ - ρ_old|| in control fes. + norm_increment = zerogf.ComputeL1Error(succ_diff_rho) + norm_reduced_gradient = norm_increment/alpha + psi_old.Assign(psi) + + compliance = (ElasticitySolver.GetParLinearForm())(u) + #compliance = MPI.COMM_WORLD.allreduce(compliance, MPI.SUM) + + if myid == 0: + print("norm of the reduced gradient = " + + "{:g}".format(norm_reduced_gradient)) + print("norm of the increment = " + "{:g}".format(norm_increment)) + print("compliance = " + "{:g}".format(compliance)) + print("volume fraction = " + + "{:g}".format(material_volume / domain_volume)) + + if visualization: + r_gf = mfem.ParGridFunction(filter_fes) + r_gf.ProjectCoefficient(SIMP_cf) + sout_r << "parallel " << num_procs << " " << myid << "\n" + sout_r << "solution\n" << pmesh << r_gf << "window_title 'Design density r(ρ̃)'" + sout_r.flush() + + if paraview_output: + rho_gf.ProjectCoefficient(rho) + paraview_dc.SetCycle(k) + paraview_dc.SetTime(float(k)) + paraview_dc.Save() + + if norm_reduced_gradient < ntol and norm_increment < itol: + break + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser(description='Ex37p (Topology Optimization)') + + parser.add_argument('-r', '--refine', + action='store', default=5, type=int, + help="Number of times to refine the mesh uniformly.") + parser.add_argument("-o", "--order", + action='store', default=2, type=int, + help="Order (degree) of the finite elements.") + parser.add_argument("-alpha", "--alpha-step-length", + action='store', default=1.0, type=float, + help="Step length for gradient descent.") + parser.add_argument("-epsilon", "--epsilon-thickness", + action='store', default=0.01, type=float, + help="Length scale for ρ.") + parser.add_argument("-mi", "--max-it", + action='store', default=1000, type=int, + help="Maximum number of gradient descent iterations.") + parser.add_argument("-ntol", "--rel-tol", + action='store', default=1e-4, type=float, + help="Normalized exit tolerance.") + parser.add_argument("-itol", "--abs-tol", + action='store', default=1e-1, type=float, + help="Increment exit tolerance.") + parser.add_argument("-vf", "--volume-fraction", + action='store', default=0.5, type=float, + help="Volume fraction for the material density.") + parser.add_argument("-lambda", "--llambda", + action='store', default=1.0, type=float, + help="Lamé constant λ.") + parser.add_argument("-mu", "--mu", + action='store', default=1.0, type=float, + help="Lamé constant μ.") + parser.add_argument("-rmin", "--psi-min", + action='store', default=1e-6, type=float, + help="Minimum of density coefficient.") + parser.add_argument("-pv", "--paraview", + action='store_true', default=False, + help="Enable or disable ParaView output.") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + + args = parser.parse_args() + + if myid == 0: + parser.print_options(args) + + globals()["visualization"] = not args.no_visualization + globals()["paraview_output"] = args.paraview + + run(ref_levels=args.refine, + order=args.order, + alpha=args.alpha_step_length, + epsilon=args.epsilon_thickness, + vol_fraction=args.volume_fraction, + max_it=args.max_it, + itol=args.abs_tol, + ntol=args.rel_tol, + rho_min=args.psi_min, + llambda=args.llambda, + mu=args.mu) diff --git a/examples/ex38.py b/examples/ex38.py new file mode 100644 index 00000000..5165b01e --- /dev/null +++ b/examples/ex38.py @@ -0,0 +1,477 @@ +''' + PyMFEM example 38 + + See c++ version in the MFEM library for more detail + + Sample runs: + python ex38.py + python ex38.py -i volumetric1d + python ex38.py -i surface2d + python ex38.py -i surface2d -o 4 -r 5 + python ex38.py -i volumetric2d + python ex38.py -i volumetric2d -o 4 -r 5 + python ex38.py -i surface3d + python ex38.py -i surface3d -o 4 -r 5 + python ex38.py -i volumetric3d + python ex38.py -i volumetric3d -o 4 -r 5 + +''' +import mfem.ser as mfem +from mfem.ser import intArray, doubleArray + +import os +from os.path import expanduser, join +import numpy as np +from numpy import sin, cos, array, pi, sqrt, floor, nan + +import numpy as np +from numba import njit +from numba.types import float64 + + +class IntegrationType: + Volumetric1D = 0 + Surface2D = 1 + Volumetric2D = 2 + Surface3D = 3 + Volumetric3D = 4 + + +visualization = True +itype = None + + +def make_lvlset_coeff(): + if itype == IntegrationType.Volumetric1D: + @mfem.jit.scalar + def func(X): + return .55 - X[0] + elif itype == IntegrationType.Surface2D: + @mfem.jit.scalar + def func(X): + return 1. - (X[0]**2 + X[1]**2) + elif itype == IntegrationType.Volumetric2D: + @mfem.jit.scalar + def func(X): + return 1. - ((X[0]/1.5)**2 + (X[1]/.75)**2) + elif itype == IntegrationType.Surface3D: + @mfem.jit.scalar + def func(X): + return 1. - (X[0]**2 + X[1]**2 + X[2]**2) + elif itype == IntegrationType.Volumetric3D: + @mfem.jit.scalar + def func(X): + return 1. - ((X[0]/1.5)**2 + (X[1]/0.75)**2 + (X[2]/.5)**2) + else: + @njit(float64(float64[:])) + def func(X): + return 1. + return func + + +def make_integrand_coeff(): + if itype == IntegrationType.Volumetric1D: + @mfem.jit.scalar + def func(X): + return 1. + elif itype == IntegrationType.Surface2D: + @mfem.jit.scalar + def func(X): + return 3. * X[0]**2 - X[1]**2 + elif itype == IntegrationType.Volumetric2D: + @mfem.jit.scalar + def func(X): + return 1. + elif itype == IntegrationType.Surface3D: + @mfem.jit.scalar + def func(X): + return 4. - 3. * X[0]**2 + 2. * X[1]**2 - X[2]**2 + elif itype == IntegrationType.Volumetric3D: + @mfem.jit.scalar + def func(X): + return 1. + else: + @mfem.jit.scalar + def func(X): + return 0. + return func + + +def Surface(): + if itype == IntegrationType.Volumetric1D: + return 1. + elif itype == IntegrationType.Surface2D: + return 2. * pi + elif itype == IntegrationType.Volumetric2D: + return 7.26633616541076 + elif itype == IntegrationType.Surface3D: + return 40. / 3. * pi + elif itype == IntegrationType.Volumetric3D: + return 9.90182151329315 + else: + return 0. + + +def Volume(): + if itype == IntegrationType.Volumetric1D: + return .55 + elif itype == IntegrationType.Surface2D: + return nan + elif itype == IntegrationType.Volumetric2D: + return 9/8*pi + elif itype == IntegrationType.Surface3D: + return nan + elif itype == IntegrationType.Volumetric3D: + return 3/4*pi + else: + return 0. + + +class SIntegrationRule(mfem.PyIntegrationRule): + def __init__(self, Order, LvlSet, lsOrder, mesh): + super(SIntegrationRule, self).__init__() + + self.Weights = mfem.DenseMatrix() + self.SurfaceWeights = mfem.DenseMatrix() + self.dim = mesh.Dimension() + + MFIRs = mfem.MomentFittingIntRules(Order, LvlSet, lsOrder) + Tr = mesh.GetElementTransformation(0) + + ir = mfem.IntegrationRule() + MFIRs.GetSurfaceIntegrationRule(Tr, ir) + if self.dim > 1: + self.Weights.SetSize(ir.GetNPoints(), mesh.GetNE()) + else: + self.Weights.SetSize(2, mesh.GetNE()) + + self.SurfaceWeights.SetSize(ir.GetNPoints(), mesh.GetNE()) + + w = mfem.Vector() + MFIRs.GetSurfaceWeights(Tr, ir, w) + self.SurfaceWeights.SetCol(0, w) + + self.SetSize(ir.GetNPoints()) + + for ip in range(self.GetNPoints()): + self.IntPoint(ip).index = ip + intp = self.IntPoint(ip) + intp.x = ir.IntPoint(ip).x + intp.y = ir.IntPoint(ip).y + intp.z = ir.IntPoint(ip).z + if self.dim > 1: + self.Weights[ip, 0] = ir.IntPoint(ip).weight + else: + self.Weights[0, 0] = ir.IntPoint(ip).x + self.Weights[1, 0] = ir.IntPoint(ip).weight + + for elem in range(mesh.GetNE()): + Tr = mesh.GetElementTransformation(elem) + MFIRs.GetSurfaceIntegrationRule(Tr, ir) + + w = mfem.Vector() + MFIRs.GetSurfaceWeights(Tr, ir, w) + self.SurfaceWeights.SetCol(elem, w) + + for ip in range(self.GetNPoints()): + if self.dim > 1: + self.Weights[ip, elem] = ir.IntPoint(ip).weight + else: + self.Weights[0, elem] = ir.IntPoint(ip).x + self.Weights[1, elem] = ir.IntPoint(ip).weight + + def SetElementinclSurfaceWeight(self, Element): + if self.dim == 1: + intp = self.IntPoint(0) + intp.x = self.Weights[0, Element] + intp.weight = self.Weights[1, Element] + print(str(intp.x) + " " + str(Element)) + else: + for ip in range(self.GetNPoints()): + intp = self.IntPoint(ip) + intp.weight = self.Weights[ip, Element] * \ + self.SurfaceWeights[ip, Element] + + def SetElement(self, Element): + if self.dim == 1: + intp = IntPoint(0) + intp.x = self.Weights[0, Element] + intp.weight = Weights[1, Element] + else: + for ip in range(self.GetNPoints()): + intp = self.IntPoint(ip) + intp.weight = self.Weights[ip, Element] + + +class CIntegrationRule(mfem.PyIntegrationRule): + def __init__(self, Order, LvlSet, lsOrder, mesh): + super(CIntegrationRule, self).__init__() + self.dim = mesh.Dimension() + self.Weights = mfem.DenseMatrix() + + MFIRs = mfem.MomentFittingIntRules(Order, LvlSet, lsOrder) + + Tr = mesh.GetElementTransformation(0) + + ir = mfem.IntegrationRule() + MFIRs.GetVolumeIntegrationRule(Tr, ir) + if self.dim > 1: + self.Weights.SetSize(ir.GetNPoints(), mesh.GetNE()) + else: + self.Weights.SetSize(2 * ir.GetNPoints(), mesh.GetNE()) + + self.SetSize(ir.GetNPoints()) + for ip in range(self.GetNPoints()): + self.IntPoint(ip).index = ip + intp = self.IntPoint(ip) + intp.x = ir.IntPoint(ip).x + intp.y = ir.IntPoint(ip).y + intp.z = ir.IntPoint(ip).z + if self.dim > 1: + self.Weights[ip, 0] = ir.IntPoint(ip).weight + else: + self.Weights[2 * ip, 0] = ir.IntPoint(ip).x + self.Weights[2 * ip + 1, 0] = ir.IntPoint(ip).weight + + for elem in range(mesh.GetNE()): + Tr = mesh.GetElementTransformation(elem) + MFIRs.GetVolumeIntegrationRule(Tr, ir) + for ip in range(self.GetNPoints()): + if self.dim > 1: + self.Weights[ip, elem] = ir.IntPoint(ip).weight + else: + self.Weights[2 * ip, elem] = ir.IntPoint(ip).x + self.Weights[2 * ip + 1, elem] = ir.IntPoint(ip).weight + + def SetElement(self, Element): + if self.dim == 1: + for ip in range(self.GetNPoints()): + intp = self.IntPoint(ip) + intp.x = self.Weights[2 * ip, Element] + intp.weight = self.Weights[2 * ip + 1, Element] + else: + for ip in range(self.GetNPoints()): + intp = self.IntPoint(ip) + intp.weight = self.Weights[ip, Element] + + +class SurfaceLFIntegrator(mfem.PyLinearFormIntegrator): + def __init__(self, q, levelset, ir): + self.Q = q + self.LevelSet = levelset + self.SIntRule = ir + self.shape = mfem.Vector() + super(SurfaceLFIntegrator, self).__init__(ir) + + def AssembleRHSElementVect(self, el, Tr, elvect): + dof = el.GetDof() + self.shape.SetSize(dof) + elvect.SetSize(dof) + elvect.Assign(0.) + + # Update the surface integration rule for the current element + self.SIntRule.SetElementinclSurfaceWeight(Tr.ElementNo) + + for ip in range(self.SIntRule.GetNPoints()): + Tr.SetIntPoint(self.SIntRule.IntPoint(ip)) + val = Tr.Weight() * self.Q.Eval(Tr, self.SIntRule.IntPoint(ip)) + el.CalcShape(self.SIntRule.IntPoint(ip), self.shape) + mfem.add_vector(elvect, self.SIntRule.IntPoint( + ip).weight * val, self.shape, elvect) + + +class SubdomainLFIntegrator(mfem.PyLinearFormIntegrator): + def __init__(self, q, levelset, ir): + self.shape = mfem.Vector() + self.CIntRule = ir + self.LevelSet = levelset + self.Q = q + super(SubdomainLFIntegrator, self).__init__(ir) + + def AssembleRHSElementVect(self, el, Tr, elvect): + dof = el.GetDof() + self.shape.SetSize(dof) + elvect.SetSize(dof) + elvect.Assign(0.) + + # Update the subdomain integration rule + self.CIntRule.SetElement(Tr.ElementNo) + for ip in range(self.CIntRule.GetNPoints()): + Tr.SetIntPoint(self.CIntRule.IntPoint(ip)) + val = Tr.Weight() * self.Q.Eval(Tr, self.CIntRule.IntPoint(ip)) + el.CalcPhysShape(Tr, self.shape) + mfem.add_vector(elvect, self.CIntRule.IntPoint( + ip).weight * val, self.shape, elvect) + + +def run(ref_levels=3, order=2): + if itype == IntegrationType.Volumetric1D: + mesh = mfem.Mesh("../data/inline-segment.mesh") + elif (itype == IntegrationType.Surface2D or + itype == IntegrationType.Volumetric2D): + mesh = mfem.Mesh(2, 4, 1, 0, 2) + mesh.AddVertex(-1.6, -1.6) + mesh.AddVertex(1.6, -1.6) + mesh.AddVertex(1.6, 1.6) + mesh.AddVertex(-1.6, 1.6) + mesh.AddQuad(0, 1, 2, 3) + mesh.FinalizeQuadMesh(1, 0, True) + elif (itype == IntegrationType.Surface3D or + itype == IntegrationType.Volumetric3D): + mesh = mfem.Mesh(3, 8, 1, 0, 3) + mesh.AddVertex(-1.6, -1.6, -1.6) + mesh.AddVertex(1.6, -1.6, -1.6) + mesh.AddVertex(1.6, 1.6, -1.6) + mesh.AddVertex(-1.6, 1.6, -1.6) + mesh.AddVertex(-1.6, -1.6, 1.6) + mesh.AddVertex(1.6, -1.6, 1.6) + mesh.AddVertex(1.6, 1.6, 1.6) + mesh.AddVertex(-1.6, 1.6, 1.6) + mesh.AddHex(0, 1, 2, 3, 4, 5, 6, 7) + mesh.FinalizeHexMesh(1, 0, True) + else: + assert False, "Unknown integration type" + + for i in range(ref_levels): + mesh.UniformRefinement() + + # 3. Define the necessary finite element space on the mesh. + fe_col = mfem.H1_FECollection(1, mesh.Dimension()) + fespace = mfem.FiniteElementSpace(mesh, fe_col) + + # 4. Construction Coefficients for the level set and the integrand. + levelset = make_lvlset_coeff() + u = make_integrand_coeff() + + # 5. Define the necessary Integration rules on element 0. + Tr = mesh.GetElementTransformation(0) + + sir = SIntegrationRule(order, levelset, 2, mesh) + if (itype == IntegrationType.Volumetric1D or + itype == IntegrationType.Volumetric2D or + itype == IntegrationType.Volumetric3D): + cir = CIntegrationRule(order, levelset, 2, mesh) + + # 6. Define and assemble the linear forms on the finite element space. + surface = mfem.LinearForm(fespace) + volume = mfem.LinearForm(fespace) + + surface.AddDomainIntegrator(SurfaceLFIntegrator(u, levelset, sir)) + surface.Assemble() + + if (itype == IntegrationType.Volumetric1D or + itype == IntegrationType.Volumetric2D or + itype == IntegrationType.Volumetric3D): + volume.AddDomainIntegrator(SubdomainLFIntegrator(u, levelset, cir)) + volume.Assemble() + + # 7. Print information, computed values and errors to the console. + qorder = 0 + nbasis = 2 * (order + 1) + (order * (order + 1) // 2) + + irs = mfem.IntegrationRules(0, mfem.Quadrature1D.GaussLegendre) + ir = irs.Get(mfem.Geometry.SQUARE, qorder) + + while (ir.GetNPoints() <= nbasis): + ir = irs.Get(mfem.Geometry.SQUARE, qorder) + qorder += 1 + + print("============================================") + if itype != IntegrationType.Volumetric1D: + print("Mesh size dx: " + + "{:g}".format(3.2 / 2**ref_levels)) + else: + print("Mesh size dx: " + + "{:g}".format(25 / 2**ref_levels)) + + if (itype == IntegrationType.Surface2D or + itype == IntegrationType.Volumetric2D): + print("Number of div free basis functions: " + str(nbasis)) + print("Number of quadrature points: " + str(ir.GetNPoints())) + + print("============================================") + print("Computed value of surface integral: " + + "{:.2e}".format(surface.Sum())) + print("True value of surface integral: " + "{:.2e}".format(Surface())) + + print("Absolut Error (Surface): " + + "{:.2e}".format(abs(surface.Sum() - Surface()))) + print("Relative Error (Surface): " + + "{:.2e}".format(abs(surface.Sum() - Surface()) / Surface())) + + if (itype == IntegrationType.Volumetric1D or + itype == IntegrationType.Volumetric2D or + itype == IntegrationType.Volumetric3D): + + print("--------------------------------------------") + print("Computed value of volume integral: " + + "{:.2e}".format(volume.Sum())) + print("True value of volume integral: " + + "{:.2e}".format(Volume())) + print("Absolut Error (Volume): " + + "{:.2e}".format(abs(volume.Sum() - Volume()))) + print("Relative Error (Volume): " + + "{:.2e}".format(abs(volume.Sum() - Volume()) / Volume())) + + print("============================================") + + # 8. Plot the level-set function on a high order finite element space. + if visualization: + fe_coll2 = mfem.H1_FECollection(5, mesh.Dimension()) + fespace2 = mfem.FiniteElementSpace(mesh, fe_coll2) + levelset_coeff = make_lvlset_coeff() + + lgf = mfem.GridFunction(fespace2) + lgf.ProjectCoefficient(levelset_coeff) + + sol_sock = mfem.socketstream("localhost", 19916) + sol_sock.precision(8) + sol_sock << "solution\n" << mesh << lgf + sol_sock.flush() + sol_sock << "keys pppppppppppppppppppppppppppcmmlRj\n" + sol_sock << "levellines " << "0." << " " << "0." << " " << 1 << "\n" + sol_sock.flush() + + +if __name__ == "__main__": + from mfem.common.arg_parser import ArgParser + + parser = ArgParser( + description='Ex38 (Cut-Volume and Cut-Surface Integration)') + + parser.add_argument("-o", "--order", + action='store', default=2, type=int, + help="Order (degree) of the finite elements.") + parser.add_argument("-r", "--refine", + action='store', default=3, type=int, + help="Number of meh refinements") + parser.add_argument("-i", "--integrationtype", + action='store', default="surface2d", type=str, + help="IntegrationType to demonstrate") + parser.add_argument("-no-vis", "--no-visualization", + action='store_true', default=False, + help='Enable GLVis visualization') + + args = parser.parse_args() + parser.print_options(args) + + globals()["visualization"] = not args.no_visualization + + if args.integrationtype.capitalize().startswith("Volumetric1"): + globals()["itype"] = IntegrationType.Volumetric1D + elif args.integrationtype.capitalize().startswith("Volumetric2"): + globals()["itype"] = IntegrationType.Volumetric2D + elif args.integrationtype.capitalize().startswith("Volumetric3"): + globals()["itype"] = IntegrationType.Volumetric3D + elif args.integrationtype.capitalize().startswith("Surface2"): + globals()["itype"] = IntegrationType.Surface2D + elif args.integrationtype.capitalize().startswith("Surface3"): + globals()["itype"] = IntegrationType.Surface3D + else: + assert False, "Unknown integration type" + + if not hasattr(mfem, "MomentFittingIntRules"): + assert False, "MFEM is not built with Lapack" + + run(ref_levels=args.refine, + order=args.order) diff --git a/mfem/__init__.py b/mfem/__init__.py index d64e8345..7cc57f1c 100644 --- a/mfem/__init__.py +++ b/mfem/__init__.py @@ -20,5 +20,5 @@ def debug_print(message): print(message) -__version__ = '4.5.2.1' +__version__ = '4.6.0.0rc1' diff --git a/mfem/_par/array.i b/mfem/_par/array.i index 470c46fb..d4c28c2d 100644 --- a/mfem/_par/array.i +++ b/mfem/_par/array.i @@ -3,10 +3,10 @@ //%rename(Equal) mfem::Array ::operator=; %{ -#include +#include #include #include -#include +#include #include "../common/io_stream.hpp" #include "mfem.hpp" #include "numpy/arrayobject.h" @@ -71,7 +71,7 @@ XXXPTR_SIZE_IN(bool *data_, int asize, bool) Array object */ mfem::Array *arr; - arr = new mfem::Array(*(int*)List_or_Tuple); + arr = new mfem::Array(*(int*)List_or_Tuple); return arr; } void __setitem__(int i, const T v) { @@ -79,7 +79,7 @@ XXXPTR_SIZE_IN(bool *data_, int asize, bool) } void Assign(const T &a){ *self = a; - } + } void FakeToList(void){} void __iter__(void){} }; @@ -115,7 +115,7 @@ def __iter__(self): raise StopIteration return iter_array(self) %} -} +} /* void Print(std::ostream &out = mfem::out, int width = 4) const; @@ -131,13 +131,46 @@ OSTREAM_ADD_DEFAULT_STDOUT_FILE(Array2D, Save) #endif namespace mfem{ -%template(doubleSwap) Swap; -%template(intSwap) Swap; +%template(doubleSwap) Swap; +%template(intSwap) Swap; } + +/* + Instantiation of Array templates. + + We instantiate some common use cases. Array.cpp instantiate these specialization. + + template class Array; + template class Array; + template class Array; + template class Array; + template class Array2D; + template class Array2D; +*/ + %import "../common/array_instantiation_macro.i" INSTANTIATE_ARRAY_INT INSTANTIATE_ARRAY_DOUBLE -IGNORE_ARRAY_METHODS(bool) +INSTANTIATE_ARRAY_NUMPYARRAY(int8, char, NPY_BYTE) // 8bit +INSTANTIATE_ARRAY_NUMPYARRAY(int64, long long, NPY_LONGLONG) // 64bit + +/* +For other classes, we need to ignore some methods + To ignore methos defined in Array.cpp, we use + IGNORE_ARRAY_METHODS_PREMITIVE + In more genral object, we need to futher ignore methods which uses comparision (> or == operators). + IGNORE_ARRAY_METHODS +*/ + +IGNORE_ARRAY_METHODS_PREMITIVE(bool) INSTANTIATE_ARRAY_BOOL +IGNORE_ARRAY_METHODS_PREMITIVE(unsigned int) +INSTANTIATE_ARRAY_NUMPYARRAY(uint, unsigned int, NPY_UINT) // 32bit +/* + for these Array2D, we instantiate it. But we dont extend it since, Array2D does not + expose the interanl pointer to array1d. +*/ +%template(intArray2D) mfem::Array2D; +%template(doubleArray2D) mfem::Array2D; diff --git a/mfem/_par/auxiliary.i b/mfem/_par/auxiliary.i index 8ec25148..91b138f4 100644 --- a/mfem/_par/auxiliary.i +++ b/mfem/_par/auxiliary.i @@ -1,12 +1,13 @@ %module (package="mfem._par") auxiliary %{ -#include +#include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pysolvers.hpp" #include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/bilinearform.i b/mfem/_par/bilinearform.i index cae8a7bc..28b20887 100644 --- a/mfem/_par/bilinearform.i +++ b/mfem/_par/bilinearform.i @@ -2,8 +2,10 @@ %{ #include "fem/bilinearform.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" using namespace mfem; %} @@ -28,32 +30,34 @@ import_array(); %import "bilininteg.i" %import "linearform.i" %import "gridfunc.i" +%import "staticcond.i" +%import "hybridization.i" %include "../common/exception_director.i" -%feature("director") mfem::BilinearForm; + //%feature("director") mfem::BilinearForm; -namespace mfem { +namespace mfem { %pythonprepend BilinearForm::AddDomainIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - bfi = args[0] + bfi = args[0] self._integrators.append(bfi) self.UseExternalIntegrators() #bfi.thisown=0 %} %pythonprepend BilinearForm::AddBoundaryIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - bfi = args[0] + bfi = args[0] self._integrators.append(bfi) self.UseExternalIntegrators() #bfi.thisown=0 - %} + %} %pythonprepend BilinearForm::AddBdrFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] bfi = args[0] self._integrators.append(bfi) self.UseExternalIntegrators() bfi.thisown=0 - %} + %} %pythonprepend BilinearForm::AddInteriorFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(bfi) @@ -68,20 +72,21 @@ namespace mfem { %pythonappend BilinearForm::EnableHybridization %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(constr_integ) - # this will be deleted by Hybridization destructor + # this will be deleted by Hybridization destructor constr_integ.thisown = 0 - %} + %} %pythonprepend MixedBilinearForm::AddDomainIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] + bfi = args[0] self._integrators.append(bfi) bfi.thisown=0 %} %pythonprepend MixedBilinearForm::AddBoundaryIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - bfi = args[0] + bfi = args[0] self._integrators.append(bfi) bfi.thisown=0 - %} + %} %pythonprepend MixedBilinearForm::AddTraceFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(bfi) @@ -89,10 +94,11 @@ namespace mfem { %} %pythonprepend MixedBilinearForm::AddBdrTraceFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - bfi = args[0] + bfi = args[0] self._integrators.append(bfi) - bfi.thisown=0 - %} + self.UseExternalIntegrators() + #bfi.thisown=0 + %} %pythonappend MixedBilinearForm::SpMat %{ if not hasattr(self, "_spmat"): self._spmat = [] self._spmat.append(val) @@ -100,32 +106,36 @@ namespace mfem { %} %pythonprepend DiscreteLinearOperator::AddDomainInterpolator %{ if not hasattr(self, "_integrators"): self._integrators = [] + di = args[0] self._integrators.append(di) di.thisown=0 - %} + %} %pythonprepend DiscreteLinearOperator::AddTraceFaceInterpolator %{ if not hasattr(self, "_integrators"): self._integrators = [] + di = args[0] self._integrators.append(di) di.thisown=0 %} - + } //end of namespace %include "fem/bilinearform.hpp" -// instatitate template methods +// instatitate template methods %define FORM_SYSTEM_MATRIX_WRAP(OsType) %template(FormLinearSystem) mfem::BilinearForm::FormLinearSystem; %template(FormSystemMatrix) mfem::BilinearForm::FormSystemMatrix; +%template(FormRectangularLinearSystem) mfem::MixedBilinearForm::FormRectangularLinearSystem; +%template(FormRectangularSystemMatrix) mfem::MixedBilinearForm::FormRectangularSystemMatrix; %enddef FORM_SYSTEM_MATRIX_WRAP(SparseMatrix) - + #ifdef MFEM_USE_MPI FORM_SYSTEM_MATRIX_WRAP(HypreParMatrix) #endif - + #ifdef MFEM_USE_PETSC FORM_SYSTEM_MATRIX_WRAP(PetscParMatrix) -#endif +#endif diff --git a/mfem/_par/bilininteg.i b/mfem/_par/bilininteg.i index e9463612..2dbae46d 100644 --- a/mfem/_par/bilininteg.i +++ b/mfem/_par/bilininteg.i @@ -1,8 +1,11 @@ %module(package="mfem._par", directors="1") bilininteg %{ #include "mfem.hpp" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pynonlininteg.hpp" #include "numpy/arrayobject.h" //using namespace mfem; %} @@ -32,11 +35,13 @@ import_array(); %import "fe.i" %import "nonlininteg.i" %include "../common/exception_director.i" - //%template(IntegrationPointArray) mfem::Array; -%feature("director") mfem::BilinearFormIntegrator; +%include "../common/bilininteg_ext.i" %ignore mfem::MassIntegrator::SetupPA; -%include "../common/bilininteg_ext.i" %include "fem/bilininteg.hpp" + +%feature("director") mfem::PyBilinearFormIntegrator; +%include "../common/pybilininteg.hpp" + diff --git a/mfem/_par/blockmatrix.i b/mfem/_par/blockmatrix.i index e0cdc229..1614891c 100644 --- a/mfem/_par/blockmatrix.i +++ b/mfem/_par/blockmatrix.i @@ -1,12 +1,12 @@ %module(package="mfem._par") blockmatrix %{ -#include +#include #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/io_stream.hpp" %} // initialization required to return numpy array from SWIG %init %{ @@ -24,7 +24,7 @@ import_array(); OSTREAM_TYPEMAP(std::ostream&) %pythonappend mfem::BlockMatrix::BlockMatrix %{ -from mfem.par import intArray +from mfem.par import intArray if len(args) == 1: if isinstance(args[0], intArray): self._offsets = args[0] diff --git a/mfem/_par/blockoperator.i b/mfem/_par/blockoperator.i index 9d5a70fc..c7fcae6c 100644 --- a/mfem/_par/blockoperator.i +++ b/mfem/_par/blockoperator.i @@ -5,8 +5,8 @@ #include "numpy/arrayobject.h" #include "linalg/operator.hpp" #include "linalg/sparsemat.hpp" -#include "linalg/hypre.hpp" -#include "pyoperator.hpp" +#include "linalg/hypre.hpp" +#include "../common/pyoperator.hpp" %} // initialization required to return numpy array from SWIG %init %{ @@ -17,7 +17,7 @@ import_array(); %import "operators.i" %pythonappend mfem::BlockOperator::BlockOperator %{ -from mfem.par import intArray +from mfem.par import intArray if len(args) == 1: if isinstance(args[0], intArray): self._offsets = args[0] @@ -30,7 +30,7 @@ if len(args) == 2: if not hasattr(self, '_linked_op'): self._linked_op = {} self._linked_op[iblock, iblock] = op -%} +%} %pythonappend mfem::BlockOperator::SetBlock %{ if not hasattr(self, '_linked_op'): self._linked_op = {} @@ -64,7 +64,7 @@ if len(args) == 2: self._linked_op = {} self._linked_op[iRow, iCol] = op -%} +%} %inline %{ mfem::BlockOperator *Opr2BlockOpr(mfem::Operator *op) { @@ -76,6 +76,6 @@ if len(args) == 2: mfem::HypreParMatrix *Opr2HypreParMat(mfem::Operator *op) { return dynamic_cast(op); } - + %} %include "linalg/blockoperator.hpp" diff --git a/mfem/_par/blockvector.i b/mfem/_par/blockvector.i index d89a3c80..ca9cc268 100644 --- a/mfem/_par/blockvector.i +++ b/mfem/_par/blockvector.i @@ -2,7 +2,7 @@ %{ #include "linalg/blockvector.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} // initialization required to return numpy array from SWIG %init %{ diff --git a/mfem/_par/coefficient.i b/mfem/_par/coefficient.i index b16f5fd4..a93d8a08 100644 --- a/mfem/_par/coefficient.i +++ b/mfem/_par/coefficient.i @@ -20,10 +20,12 @@ #include #include #include -#include "mfem.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %include "../common/mfem_config.i" @@ -58,10 +60,10 @@ namespace mfem { if can_np_array: v = mfem._par.vector.Vector(np.transpose(value).flatten()) - m = mfem._par.densemat.DenseMatrix(v.GetData(), value.shape[0], value.shape[1]) + m = mfem._par.densemat.DenseMatrix(v.GetData(), value.shape[0], value.shape[1]) self._value = (v,m) else: - pass + pass %} %pythonprepend VectorConstantCoefficient::VectorConstantCoefficient(const Vector &v) %{ try: @@ -75,7 +77,7 @@ namespace mfem { v = mfem._par.vector.Vector(value) self._value = v else: - pass + pass %} } %include "../common/coefficient_common.i" @@ -93,12 +95,12 @@ namespace mfem { %exception { try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } + catch (Swig::DirectorException &e) { SWIG_fail; } //catch (...){ // SWIG_fail; //} // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } + // catch (std::exception &e) { SWIG_fail; } } %feature("director:except") { if ($error != NULL) { @@ -140,7 +142,7 @@ void fake_func_mat(const mfem::Vector &x, mfem::DenseMatrix &Kt) Kt(2,2) = 1.0; } -namespace mfem{ +namespace mfem{ double PyCoefficientBase::Eval(ElementTransformation &T, const IntegrationPoint &ip) { @@ -169,7 +171,7 @@ void VectorPyCoefficientBase::Eval(Vector &V, ElementTransformation &T, V.SetSize(vdim); if (isTimeDependent) { - _EvalPyT(transip, GetTime(), V); + _EvalPyT(transip, GetTime(), V); } else { @@ -199,10 +201,10 @@ void MatrixPyCoefficientBase::Eval(DenseMatrix &K, ElementTransformation &T, Vector transip(x, 3); T.Transform(ip, transip); - K.SetSize(height, width); + K.SetSize(height, width); if (isTimeDependent) { - _EvalPyT(transip, GetTime(), K); + _EvalPyT(transip, GetTime(), K); } else { @@ -223,7 +225,7 @@ class PyCoefficient(PyCoefficientBase): return self.EvalValue(x.GetDataArray()) def EvalValue(self, x): return 0.0 - + class PyCoefficientT(PyCoefficientBase): def __init__(self): PyCoefficientBase.__init__(self, 1) @@ -231,25 +233,25 @@ class PyCoefficientT(PyCoefficientBase): return self.EvalValue(x.GetDataArray(), t) def EvalValue(self, x, t): return 0.0 - + class VectorPyCoefficient(VectorPyCoefficientBase): def __init__(self, dim): self.vdim = dim VectorPyCoefficientBase.__init__(self, dim, 0) def _EvalPy(self, x, V): v = self.EvalValue(x.GetDataArray()) - V.Assign(v) + V.Assign(v) def _EvalPyT(self, x, t, V): v = self.EvalValue(x.GetDataArray()) - V.Assign(v) + V.Assign(v) def EvalValue(self, x): return [0,0,0] - + class VectorPyCoefficientT(VectorPyCoefficientBase): def __init__(self, dim): - self.vdim = dim + self.vdim = dim VectorPyCoefficientBase.__init__(self, dim, 1) def _EvalPy(self, x, V): v = self.EvalValue(x.GetDataArray(), 0) @@ -257,7 +259,7 @@ class VectorPyCoefficientT(VectorPyCoefficientBase): def _EvalPyT(self, x, t, V): v = self.EvalValue(x.GetDataArray(), t) - V.Assign(v) + V.Assign(v) def EvalValue(self, x, t): return [0.0,0.0,0.0] @@ -268,21 +270,21 @@ class MatrixPyCoefficient(MatrixPyCoefficientBase): MatrixPyCoefficientBase.__init__(self, dim, 0) def _EvalPy(self, x, K): k = self.EvalValue(x.GetDataArray()) - K.Assign(k) + K.Assign(k) def EvalValue(self, x): return np.array([[0,0,0], [0,0,0], [0,0,0]]) - + class MatrixPyCoefficientT(MatrixPyCoefficientBase): def __init__(self, dim): - self.vdim = dim + self.vdim = dim MatrixPyCoefficientBase.__init__(self, dim, 1) def _EvalPyT(self, x, t, K): k = self.EvalValue(x.GetDataArray(), t) - K.Assign(k) + K.Assign(k) def EvalValue(self, x, t): return np.array([[0.0,0.0,0.0], [0.0,0.0,0.0], [0.0,0.0,0.0]]) - + %} diff --git a/mfem/_par/common_functions.i b/mfem/_par/common_functions.i index 68c63e83..1868d956 100644 --- a/mfem/_par/common_functions.i +++ b/mfem/_par/common_functions.i @@ -3,9 +3,9 @@ %{ #include #include "mfem.hpp" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/communication.i b/mfem/_par/communication.i index 6e2e0460..e70db6af 100644 --- a/mfem/_par/communication.i +++ b/mfem/_par/communication.i @@ -3,7 +3,7 @@ %{ #include -#include +#include #include #include "../common/io_stream.hpp" #include "mfem.hpp" diff --git a/mfem/_par/complex_fem.i b/mfem/_par/complex_fem.i index 1cb19da6..5bbfad95 100644 --- a/mfem/_par/complex_fem.i +++ b/mfem/_par/complex_fem.i @@ -6,11 +6,14 @@ %module(package="mfem._par") complex_fem %feature("autodoc", "1"); %{ -#include "fem/complex_fem.hpp" +#include "fem/complex_fem.hpp" #include "linalg/complex_operator.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pylininteg.hpp" %} %init %{ import_array(); diff --git a/mfem/_par/complex_operator.i b/mfem/_par/complex_operator.i index c568404d..0a4bd8f5 100644 --- a/mfem/_par/complex_operator.i +++ b/mfem/_par/complex_operator.i @@ -8,8 +8,8 @@ %{ #include "linalg/complex_operator.hpp" #include "numpy/arrayobject.h" -#include "linalg/hypre.hpp" -#include "pyoperator.hpp" +#include "linalg/hypre.hpp" +#include "../common/pyoperator.hpp" %} %include "../common/mfem_config.i" @@ -29,14 +29,14 @@ import_array(); %import "operators.i" %import "sparsemat.i" -namespace mfem { +namespace mfem { %pythonprepend ComplexOperator::ComplexOperator %{ self._parts = [Op_Real, Op_Imag] if ownReal: assert Op_Real.thisown != 0, "Real Op is not owned by passed object" Op_Real.thisown = 0 if ownImag: - assert Op_Real.thisown != 0, "Imag Op is not owned by passed object" + assert Op_Real.thisown != 0, "Imag Op is not owned by passed object" Op_Imag.thisown = 0 %} %ignore ComplexOperator::ComplexOperator(Operator * Op_Real, Operator * Op_Imag, diff --git a/mfem/_par/constraints.i b/mfem/_par/constraints.i index 2018e754..a2b7051d 100644 --- a/mfem/_par/constraints.i +++ b/mfem/_par/constraints.i @@ -6,11 +6,12 @@ %module(package="mfem._par") constraints %feature("autodoc", "1"); %{ -#include "mfem.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" #include "../common/pysolvers.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/datacollection.i b/mfem/_par/datacollection.i index 155256f3..b1e94cc6 100644 --- a/mfem/_par/datacollection.i +++ b/mfem/_par/datacollection.i @@ -1,9 +1,10 @@ %module(package="mfem._par") datacollection %{ #include "mfem.hpp" -#include "pyoperator.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/densemat.i b/mfem/_par/densemat.i index 41266bb8..4635d627 100644 --- a/mfem/_par/densemat.i +++ b/mfem/_par/densemat.i @@ -11,9 +11,9 @@ #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/io_stream.hpp" -using namespace mfem; +using namespace mfem; %} // initialization required to return numpy array from SWIG %init %{ @@ -53,9 +53,9 @@ from numpy import ndarray, ascontiguousarray keep_link = False if len(args) == 1 and isinstance(args[0], ndarray): if args[0].dtype != 'float64': - raise ValueError('Must be float64 array:' + str(args[0].dtype) + ' was given') + raise ValueError('Must be float64 array:' + str(args[0].dtype) + ' was given') elif args[0].ndim != 2: - raise ValueError('Ndim must be two') + raise ValueError('Ndim must be two') elif args[0].shape[1] != _densemat.DenseMatrix_Size(self): raise ValueError('Length does not match') else: @@ -72,23 +72,23 @@ if len(args) == 1 and isinstance(args[0], ndarray): def __iadd__(self, v): ret = _densemat.DenseMatrix___iadd__(self, v) ret.thisown = self.thisown - self.thisown = 0 + self.thisown = 0 return ret %} %feature("shadow") mfem::DenseMatrix::operator-= %{ def __isub__(self, v): - ret = _densemat.DenseMatrix___isub__(self, v) + ret = _densemat.DenseMatrix___isub__(self, v) ret.thisown = self.thisown - self.thisown = 0 + self.thisown = 0 return ret -%} +%} %feature("shadow") mfem::DenseMatrix::operator*= %{ def __imul__(self, v): - ret = _densemat.DenseMatrix___imul__(self, v) + ret = _densemat.DenseMatrix___imul__(self, v) ret.thisown = self.thisown - self.thisown = 0 + self.thisown = 0 return ret -%} +%} %feature("shadow") mfem::DenseMatrix::__setitem__%{ def __setitem__(self, *args): i, j, v = args[0][0], args[0][1], args[1] @@ -117,9 +117,9 @@ def __getitem__(self, *args): check = int(args[0]) except: check = -1 - if check >= 0: + if check >= 0: return _densemat.DenseTensor___getitem__(self, check) -%} +%} %include "linalg/densemat.hpp" @@ -142,11 +142,11 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data NDIM must be 2"); return NULL; } - npy_intp *shape = PyArray_DIMS(numpymat0); + npy_intp *shape = PyArray_DIMS(numpymat0); return new mfem::DenseMatrix(shape[0], shape[1]); } - + void Assign(const double v) { (* self) = v; } @@ -160,7 +160,7 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data must be ndarray"); return; } - PyArrayObject *numpymat0 = reinterpret_cast(numpymat); + PyArrayObject *numpymat0 = reinterpret_cast(numpymat); int typ = PyArray_TYPE(numpymat0); if (typ != NPY_DOUBLE){ PyErr_SetString(PyExc_ValueError, "Input data must be float64"); @@ -173,19 +173,19 @@ def __getitem__(self, *args): } npy_intp *shape = PyArray_DIMS(numpymat0); int len = self->Width()*self->Height(); - if (shape[1]*shape[0] != len){ + if (shape[1]*shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; } - PyObject * tmp1 = + PyObject * tmp1 = PyArray_Transpose(numpymat0, NULL); - PyArrayObject * tmp2 = + PyArrayObject * tmp2 = PyArray_GETCONTIGUOUS((PyArrayObject *)tmp1); (* self) = (double *) PyArray_DATA(tmp2); Py_XDECREF(tmp1); - Py_XDECREF(tmp2); + Py_XDECREF(tmp2); } - + const double __getitem__(const int i, const int j) const{ return (* self)(i, j); } @@ -193,7 +193,7 @@ def __getitem__(self, *args): (* self)(i, j) = v; } PyObject* GetDataArray(void) const{ - double * A = self->Data(); + double * A = self->Data(); npy_intp dims[] = {self->Width(), self->Height()}; PyObject *tmp1 = PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, A); PyObject *ret = PyArray_Transpose((PyArrayObject *)tmp1, NULL); @@ -228,16 +228,16 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data NDIM must be 3"); return ; } - npy_intp *shape = PyArray_DIMS(numpymat0); + npy_intp *shape = PyArray_DIMS(numpymat0); int len = self->SizeI()*self->SizeJ()*self->SizeK(); - if (shape[2]*shape[1]*shape[0] != len){ + if (shape[2]*shape[1]*shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; } for (int i=0; i < self->SizeI(); i++){ for (int j=0; j < self->SizeJ(); j++){ - for (int k=0; k < self->SizeK(); k++){ + for (int k=0; k < self->SizeK(); k++){ (* self)(i, j, k) = *(double *) PyArray_GETPTR3(numpymat0, i, j, k); } } @@ -254,12 +254,12 @@ def __getitem__(self, *args): } PyObject* GetDataArray(void){ // DoDo this method can not be const since DenseTensor::Data is not const - double * A = self->Data(); + double * A = self->Data(); npy_intp dims[] = {self->SizeK(), self->SizeJ(), self->SizeI()}; PyObject * obj = PyArray_SimpleNewFromData(3, dims, NPY_DOUBLE, A); //obj = PyArray_SwapAxes((PyArrayObject *)obj, 0, 2); PyObject * ret = PyArray_SwapAxes((PyArrayObject *)obj, 1, 2); - Py_XDECREF(obj); + Py_XDECREF(obj); return ret; } }; diff --git a/mfem/_par/device.i b/mfem/_par/device.i index 08a49da6..c7cfe7fe 100644 --- a/mfem/_par/device.i +++ b/mfem/_par/device.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/device.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ @@ -25,7 +25,7 @@ import_array(); %} %feature("shadow") mfem::Device::__new__ %{ def __new__(cls, *args, **kwargs): - if globals()["singleton_device"] is None: + if globals()["singleton_device"] is None: instance = super(Device, cls).__new__(cls) globals()["singleton_device"] = instance return globals()["singleton_device"] @@ -37,7 +37,7 @@ import_array(); %include "general/device.hpp" %extend mfem::Device{ - // placeholder to create __new__ + // placeholder to create __new__ void __new__(void){} }; diff --git a/mfem/_par/dist_solver.i b/mfem/_par/dist_solver.i index 380979a1..c3d8cbd9 100644 --- a/mfem/_par/dist_solver.i +++ b/mfem/_par/dist_solver.i @@ -1,11 +1,14 @@ %module(package="mfem._par") dist_solver %{ -#include "mfem.hpp" +#include "mfem.hpp" +#include "numpy/arrayobject.h" #include "miniapps/common/dist_solver.hpp" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pysolvers.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pynonlininteg.hpp" %} %init %{ diff --git a/mfem/_par/doftrans.i b/mfem/_par/doftrans.i index ba052187..549582bf 100644 --- a/mfem/_par/doftrans.i +++ b/mfem/_par/doftrans.i @@ -1,15 +1,17 @@ %module(package="mfem._par") doftrans %{ -#include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ import_array(); %} %include "exception.i" -%import "fe.i" +%import "vector.i" +%import "densemat.i" %import "intrules.i" %include "../common/typemap_macros.i" %include "../common/exception.i" diff --git a/mfem/_par/element.i b/mfem/_par/element.i index 6e4ad0aa..ed883f96 100644 --- a/mfem/_par/element.i +++ b/mfem/_par/element.i @@ -1,10 +1,11 @@ %module(package="mfem._par") element - + %{ -#include +#include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/eltrans.i b/mfem/_par/eltrans.i index b0e8fc75..08b9f71a 100644 --- a/mfem/_par/eltrans.i +++ b/mfem/_par/eltrans.i @@ -2,9 +2,10 @@ %{ #include "mfem.hpp" -#include "pyoperator.hpp" #include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/error.i b/mfem/_par/error.i index 5145a20a..8ca25982 100644 --- a/mfem/_par/error.i +++ b/mfem/_par/error.i @@ -1,9 +1,9 @@ %module(package="mfem._par") error %{ -#include +#include #include #include -#include "general/error.hpp" +#include "general/error.hpp" %} %include "exception.i" %include "../common/exception.i" diff --git a/mfem/_par/estimators.i b/mfem/_par/estimators.i index b37cceb2..10184fb4 100644 --- a/mfem/_par/estimators.i +++ b/mfem/_par/estimators.i @@ -1,9 +1,11 @@ %module(package="mfem._par") estimators %{ #include "mfem.hpp" -#include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %include "../common/mfem_config.i" @@ -54,7 +56,7 @@ namespace mfem{ } /* this is to ignroe final keyword */ -#define final +#define final %include "fem/estimators.hpp" @@ -75,7 +77,7 @@ namespace mfem{ L2ZienkiewiczZhuEstimator(mfem::BilinearFormIntegrator &integ, mfem::ParGridFunction &sol, mfem::ParFiniteElementSpace *flux_fes, - mfem::ParFiniteElementSpace *smooth_flux_fes, + mfem::ParFiniteElementSpace *smooth_flux_fes, bool own_flux_fes = false){ if (own_flux_fes){ return new mfem::L2ZienkiewiczZhuEstimator(integ, sol, diff --git a/mfem/_par/fe.i b/mfem/_par/fe.i index 485234a1..d9a51677 100644 --- a/mfem/_par/fe.i +++ b/mfem/_par/fe.i @@ -1,10 +1,11 @@ %module (package="mfem._par") fe %{ -#include +#include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_base.i b/mfem/_par/fe_base.i index a7d09750..dac6b233 100644 --- a/mfem/_par/fe_base.i +++ b/mfem/_par/fe_base.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_base %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -11,6 +12,7 @@ import_array(); %include "exception.i" %import "intrules.i" %import "geom.i" +%import "doftrans.i" %include "../common/typemap_macros.i" %include "../common/exception.i" diff --git a/mfem/_par/fe_coll.i b/mfem/_par/fe_coll.i index af9894ed..8cdf51b3 100644 --- a/mfem/_par/fe_coll.i +++ b/mfem/_par/fe_coll.i @@ -7,10 +7,11 @@ #include #include #include -#include "mfem.hpp" -#include "pyoperator.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -32,4 +33,4 @@ import_array(); %include "fem/fe_coll.hpp" %pythoncode %{ DG_FECollection = L2_FECollection -%} +%} diff --git a/mfem/_par/fe_fixed_order.i b/mfem/_par/fe_fixed_order.i index 99abb108..ef7e15d8 100644 --- a/mfem/_par/fe_fixed_order.i +++ b/mfem/_par/fe_fixed_order.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_fixed_order %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_h1.i b/mfem/_par/fe_h1.i index 1349a626..551ab0cc 100644 --- a/mfem/_par/fe_h1.i +++ b/mfem/_par/fe_h1.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_h1 %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_l2.i b/mfem/_par/fe_l2.i index f00f4948..9581a46e 100644 --- a/mfem/_par/fe_l2.i +++ b/mfem/_par/fe_l2.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_l2 %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_nd.i b/mfem/_par/fe_nd.i index f385a0f8..6828397d 100644 --- a/mfem/_par/fe_nd.i +++ b/mfem/_par/fe_nd.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_nd %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_nurbs.i b/mfem/_par/fe_nurbs.i index e0ec3e3c..d24a893c 100644 --- a/mfem/_par/fe_nurbs.i +++ b/mfem/_par/fe_nurbs.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_nurbs %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_pos.i b/mfem/_par/fe_pos.i index eb2ff767..91a8266c 100644 --- a/mfem/_par/fe_pos.i +++ b/mfem/_par/fe_pos.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_pos %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_rt.i b/mfem/_par/fe_rt.i index 3a35c37c..656f606a 100644 --- a/mfem/_par/fe_rt.i +++ b/mfem/_par/fe_rt.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_rt %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fe_ser.i b/mfem/_par/fe_ser.i index 85110f14..cbf350db 100644 --- a/mfem/_par/fe_ser.i +++ b/mfem/_par/fe_ser.i @@ -1,8 +1,9 @@ %module(package="mfem._par") fe_ser %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/fespace.i b/mfem/_par/fespace.i index 0b1d22fc..558381b0 100644 --- a/mfem/_par/fespace.i +++ b/mfem/_par/fespace.i @@ -10,17 +10,12 @@ #include #include #include -#include "fem/fem.hpp" -#include "fem/fe_coll.hpp" -#include "fem/fespace.hpp" -#include "fem/eltrans.hpp" -#include "fem/coefficient.hpp" -#include "fem/intrules.hpp" -#include "fem/restriction.hpp" -#include "../common/io_stream.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -167,7 +162,7 @@ def GetEdgeInteriorDofs(self, i): if hasattr(self, 'this'): self.mesh = args[0] self.fec = args[1] - + %} /* define FiniteElementSpacePtrArray */ @@ -200,11 +195,11 @@ OSTREAM_ADD_DEFAULT_STDOUT_FILE(QuadratureSpace, Save) return self->GetBdrElementDofs(bel, dofs); } virtual DofTransformation *GetElementVDofTransformation(int elem) const { - mfem::Array dofs; + mfem::Array dofs; return self->GetElementVDofs(elem, dofs); } virtual DofTransformation *GetBdrElementVDofTransformation(int bel) const { - mfem::Array dofs; + mfem::Array dofs; return self->GetBdrElementVDofs(bel, dofs); } }; diff --git a/mfem/_par/fespacehierarchy.i b/mfem/_par/fespacehierarchy.i index 430bb67e..75dbcacc 100644 --- a/mfem/_par/fespacehierarchy.i +++ b/mfem/_par/fespacehierarchy.i @@ -8,8 +8,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ import_array(); diff --git a/mfem/_par/geom.i b/mfem/_par/geom.i index 5e6df1c8..2b25eb47 100644 --- a/mfem/_par/geom.i +++ b/mfem/_par/geom.i @@ -2,8 +2,10 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ diff --git a/mfem/_par/globals.i b/mfem/_par/globals.i index bf70593c..b922462b 100644 --- a/mfem/_par/globals.i +++ b/mfem/_par/globals.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/globals.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_par/gridfunc.i b/mfem/_par/gridfunc.i index b74373ba..69672a10 100644 --- a/mfem/_par/gridfunc.i +++ b/mfem/_par/gridfunc.i @@ -1,17 +1,20 @@ %module(package="mfem._par", directors="0") gridfunc %{ - #include + #include #include #include #include #include #include #include - #include "mfem/mfem.hpp" - #include "../common/pycoefficient.hpp" - #include "pyoperator.hpp" + #include "mfem/mfem.hpp" #include "numpy/arrayobject.h" #include "../common/io_stream.hpp" + #include "../common/pycoefficient.hpp" + #include "../common/pyoperator.hpp" + #include "../common/pyintrules.hpp" + #include "../common/pybilininteg.hpp" + using namespace mfem; %} @@ -69,12 +72,12 @@ def GetNodalValues(self, *args): $1 = (mfem::IntegrationRule **) malloc((size)*sizeof(mfem::IntegrationRule *)); for (i = 0; i < size; i++) { PyObject *o = PyList_GetItem($input,i); - void *temp; + void *temp; if (SWIG_ConvertPtr(o, &temp, $descriptor(mfem::IntegrationRule *),SWIG_POINTER_EXCEPTION) == -1){ return NULL; } - $1[i] = reinterpret_cast(temp); + $1[i] = reinterpret_cast(temp); } } else { PyErr_SetString(PyExc_TypeError,"not a list"); @@ -95,9 +98,9 @@ LIST_TO_MFEMOBJ_POINTERARRAY_IN(mfem::IntegrationRule const *irs[], mfem::Integ namespace mfem{ %extend GridFunction{ - + GridFunction(mfem::FiniteElementSpace *fes, const mfem::Vector &v, int offset){ - mfem::GridFunction *gf; + mfem::GridFunction *gf; gf = new mfem::GridFunction(fes, v.GetData() + offset); return gf; } @@ -109,12 +112,12 @@ GridFunction(mfem::FiniteElementSpace *fes, const mfem::Vector &v, int offset){ } void Assign(const mfem::GridFunction &v) { (* self) = v; - } + } void Assign(PyObject* param) { /* note that these error does not raise error in python type check is actually done in wrapper layer */ PyArrayObject *param0 = reinterpret_cast(param); - + if (!PyArray_Check(param0)){ PyErr_SetString(PyExc_ValueError, "Input data must be ndarray"); return; @@ -129,21 +132,21 @@ GridFunction(mfem::FiniteElementSpace *fes, const mfem::Vector &v, int offset){ PyErr_SetString(PyExc_ValueError, "Input data NDIM must be one"); return ; } - npy_intp *shape = PyArray_DIMS(param0); + npy_intp *shape = PyArray_DIMS(param0); int len = self->Size(); - if (shape[0] != len){ + if (shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; - } + } (Vector &)(* self) = (double *) PyArray_DATA(param0); } void SaveToFile(const char *gf_file, const int precision) const { - std::cerr << "\nWarning Deprecated : Use Save(filename) insteead of SaveToFile \n"; - std::ofstream mesh_ofs(gf_file); + std::cerr << "\nWarning Deprecated : Use Save(filename) insteead of SaveToFile \n"; + std::ofstream mesh_ofs(gf_file); mesh_ofs.precision(precision); - self->Save(mesh_ofs); + self->Save(mesh_ofs); } PyObject* WriteToStream(PyObject* StringIO) const { @@ -151,12 +154,12 @@ PyObject* WriteToStream(PyObject* StringIO) const { if (!module){ PyErr_SetString(PyExc_RuntimeError, "Can not load io module"); return (PyObject *) NULL; - } + } PyObject* cls = PyObject_GetAttrString(module, "StringIO"); if (!cls){ PyErr_SetString(PyExc_RuntimeError, "Can not load StringIO"); return (PyObject *) NULL; - } + } int check = PyObject_IsInstance(StringIO, cls); Py_DECREF(module); if (! check){ @@ -173,9 +176,9 @@ PyObject* WriteToStream(PyObject* StringIO) const { PyErr_SetString(PyExc_RuntimeError, "Error occured when writing IOString"); return (PyObject *) NULL; } - return ret; + return ret; } - +/* GridFunction & iadd(GridFunction &c) { *self += c; @@ -201,9 +204,11 @@ GridFunction & idiv(double c) * self /= c; return *self; } - } +*/ + } // end of extend } // end of namespace +/* %pythoncode %{ def __iadd__(self, v): ret = _gridfunc.GridFunction_iadd(self, v) @@ -221,13 +226,13 @@ def __imul__(self, v): ret = _gridfunc.GridFunction_imul(self, v) ret.thisown = 0 return self - + GridFunction.__iadd__ = __iadd__ GridFunction.__idiv__ = __idiv__ GridFunction.__isub__ = __isub__ -GridFunction.__imul__ = __imul__ -%} - +GridFunction.__imul__ = __imul__ +%} +*/ /* fem/gridfunc.hpp: virtual void Save(std::ostream &out) const; fem/gridfunc.hpp: void Save(std::ostream &out) const; @@ -240,4 +245,4 @@ fem/gridfunc.hpp: void SaveSTL(std::ostream &out, int TimesToRefine = 1); OSTREAM_ADD_DEFAULT_FILE(GridFunction, Save) OSTREAM_ADD_DEFAULT_FILE(QuadratureFunction, Save) - + diff --git a/mfem/_par/gslib.i b/mfem/_par/gslib.i index 920685b2..72efde7f 100644 --- a/mfem/_par/gslib.i +++ b/mfem/_par/gslib.i @@ -3,8 +3,9 @@ #include "mfem.hpp" #include "fem/gslib.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/handle.i b/mfem/_par/handle.i index f83829b8..2a863553 100644 --- a/mfem/_par/handle.i +++ b/mfem/_par/handle.i @@ -1,17 +1,17 @@ %module(package="mfem._par") handle %feature("autodoc", "1"); %{ -#include +#include #include -#include "../common/io_stream.hpp" -#include "config/config.hpp" +#include "../common/io_stream.hpp" +#include "config/config.hpp" #include "linalg/hypre.hpp" -#include "linalg/handle.hpp" -#include "fem/gridfunc.hpp" +#include "linalg/handle.hpp" +#include "fem/gridfunc.hpp" #include "fem/linearform.hpp" #include "fem/pfespace.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} %include "../common/mfem_config.i" @@ -50,14 +50,14 @@ GET_RENAME(SparseMatrix) RESET_RENAME(SparseMatrix) CONVERT_FROM_RENAME(SparseMatrix) - //CONSTRUCTOR_RENAME(HypreParMatrix) + //CONSTRUCTOR_RENAME(HypreParMatrix) AS_RENAME(HypreParMatrix) IS_RENAME(HypreParMatrix) GET_RENAME(HypreParMatrix) RESET_RENAME(HypreParMatrix) CONVERT_FROM_RENAME(HypreParMatrix) -//CONSTRUCTOR_RENAME(ComplexHypreParMatrix) +//CONSTRUCTOR_RENAME(ComplexHypreParMatrix) AS_RENAME(ComplexHypreParMatrix) IS_RENAME(ComplexHypreParMatrix) GET_RENAME(ComplexHypreParMatrix) @@ -65,18 +65,18 @@ RESET_RENAME(ComplexHypreParMatrix) CONVERT_FROM_RENAME(ComplexHypreParMatrix) #ifdef MFEM_USE_PETSC - //CONSTRUCTOR_RENAME(PetscParMatrix) + //CONSTRUCTOR_RENAME(PetscParMatrix) AS_RENAME(PetscParMatrix) IS_RENAME(PetscParMatrix) GET_RENAME(PetscParMatrix) RESET_RENAME(PetscParMatrix) -CONVERT_FROM_RENAME(PetscParMatrix) +CONVERT_FROM_RENAME(PetscParMatrix) #endif %include "linalg/handle.hpp" %pythoncode %{ -OperatorPtr=OperatorHandle +OperatorPtr=OperatorHandle %} // instatitate template methods (step 2: Instantiation) @@ -84,29 +84,29 @@ OperatorPtr=OperatorHandle AS_WRAP(SparseMatrix) IS_WRAP(SparseMatrix) GET_WRAP(SparseMatrix) -RESET_WRAP(SparseMatrix) +RESET_WRAP(SparseMatrix) CONVERT_FROM_WRAP(SparseMatrix) -//CONSTRUCTOR_WRAP(HypreParMatrix) +//CONSTRUCTOR_WRAP(HypreParMatrix) AS_WRAP(HypreParMatrix) IS_WRAP(HypreParMatrix) GET_WRAP(HypreParMatrix) -RESET_WRAP(HypreParMatrix) +RESET_WRAP(HypreParMatrix) CONVERT_FROM_WRAP(HypreParMatrix) -//CONSTRUCTOR_WRAP(ComplexHypreParMatrix) +//CONSTRUCTOR_WRAP(ComplexHypreParMatrix) AS_WRAP(ComplexHypreParMatrix) IS_WRAP(ComplexHypreParMatrix) GET_WRAP(ComplexHypreParMatrix) -RESET_WRAP(ComplexHypreParMatrix) +RESET_WRAP(ComplexHypreParMatrix) CONVERT_FROM_WRAP(ComplexHypreParMatrix) - + #ifdef MFEM_USE_PETSC -//CONSTRUCTOR_WRAP(PetscParMatrix) +//CONSTRUCTOR_WRAP(PetscParMatrix) AS_WRAP(PetscParMatrix) IS_WRAP(PetscParMatrix) GET_WRAP(PetscParMatrix) -RESET_WRAP(PetscParMatrix) +RESET_WRAP(PetscParMatrix) CONVERT_FROM_WRAP(PetscParMatrix) #endif - + diff --git a/mfem/_par/hexahedron.i b/mfem/_par/hexahedron.i index d6526ae9..6796766a 100644 --- a/mfem/_par/hexahedron.i +++ b/mfem/_par/hexahedron.i @@ -1,8 +1,9 @@ %module(package="mfem._par") hexahedron %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/hybridization.i b/mfem/_par/hybridization.i index 486d94ca..addf12e2 100644 --- a/mfem/_par/hybridization.i +++ b/mfem/_par/hybridization.i @@ -1,9 +1,11 @@ %module(package="mfem._par") hybridization %{ #include "mfem.hpp" -#include "pyoperator.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ diff --git a/mfem/_par/hypre.i b/mfem/_par/hypre.i index 2f228d32..617d719b 100644 --- a/mfem/_par/hypre.i +++ b/mfem/_par/hypre.i @@ -2,17 +2,17 @@ %feature("autodoc", "1"); %{ #include -#include +#include #include #include #include "fem/gridfunc.hpp" #include "fem/linearform.hpp" -#include "fem/pfespace.hpp" -#include "config/config.hpp" +#include "fem/pfespace.hpp" +#include "config/config.hpp" #include "linalg/hypre.hpp" -#include "linalg/hypre_parcsr.hpp" +#include "linalg/hypre_parcsr.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/io_stream.hpp" %} @@ -51,7 +51,7 @@ int sizeof_HYPRE_Int(){ int sizeof_HYPRE_BigInt(){ return sizeof(HYPRE_BigInt); } -bool is_HYPRE_USING_CUDA(){ +bool is_HYPRE_USING_CUDA(){ #ifdef HYPRE_USING_CUDA return true; #else @@ -61,7 +61,7 @@ bool is_HYPRE_USING_CUDA(){ %} /* - support numpy array input to + support numpy array input to HypreParVector(MPI_Comm comm, HYPRE_Int glob_size, double *_data, HYPRE_Int *col); @@ -71,7 +71,7 @@ bool is_HYPRE_USING_CUDA(){ // We keep reference to such outside numpy array in ProxyClass tmp_arr1_ = (PyArrayObject *)PyList_GetItem($input,0); tmp_arr2_ = (PyArrayObject *)PyList_GetItem($input,1); - + $1 = (double *) PyArray_DATA(tmp_arr1_); $2 = (HYPRE_BigInt *) PyArray_DATA(tmp_arr2_); } @@ -85,12 +85,12 @@ bool is_HYPRE_USING_CUDA(){ $1 = 1; if (!PyArray_Check(PyList_GetItem($input,0))) $1 = 0; if (!PyArray_Check(PyList_GetItem($input,1))) $1 = 0; - } else $1 = 0; + } else $1 = 0; } } /* - support numpy array input to + support numpy array input to HypreParMatrix(MPI_Comm comm, int nrows, HYPRE_Int glob_nrows, HYPRE_Int glob_ncols, int *I, HYPRE_Int *J, double *data, HYPRE_Int *rows, HYPRE_Int *cols); @@ -98,7 +98,7 @@ bool is_HYPRE_USING_CUDA(){ note that if cols and rows are the same (as a pointer), hypre_CSRMatrixReorder is called. It is not clear how to say "same as pointer" in Python. Here, if the list length - is 4, cols is set to be rows. + is 4, cols is set to be rows. */ %typemap(in) (int *I, @@ -111,13 +111,13 @@ bool is_HYPRE_USING_CUDA(){ PyArrayObject *tmp_arr3_ = NULL, PyArrayObject *tmp_arr4_ = NULL, PyArrayObject *tmp_arr5_ = NULL, int list_len_=0){ - + tmp_arr1_ = PyArray_GETCONTIGUOUS((PyArrayObject *)PyList_GetItem($input,0)); tmp_arr2_ = PyArray_GETCONTIGUOUS((PyArrayObject *)PyList_GetItem($input,1)); tmp_arr3_ = PyArray_GETCONTIGUOUS((PyArrayObject *)PyList_GetItem($input,2)); tmp_arr4_ = PyArray_GETCONTIGUOUS((PyArrayObject *)PyList_GetItem($input,3)); list_len_ = PyList_Size($input); - if (list_len_ == 5){ + if (list_len_ == 5){ tmp_arr5_ = PyArray_GETCONTIGUOUS((PyArrayObject *)PyList_GetItem($input,4)); } $1 = (int *) PyArray_DATA(tmp_arr1_); @@ -133,7 +133,7 @@ bool is_HYPRE_USING_CUDA(){ %typemap(freearg) (int *I, HYPRE_BigInt *J, double *data, HYPRE_BigInt *rows, HYPRE_BigInt *cols){ Py_XDECREF(tmp_arr1_$argnum); - Py_XDECREF(tmp_arr2_$argnum); + Py_XDECREF(tmp_arr2_$argnum); Py_XDECREF(tmp_arr3_$argnum); Py_XDECREF(tmp_arr4_$argnum); if (list_len_$argnum == 5){ @@ -160,7 +160,7 @@ bool is_HYPRE_USING_CUDA(){ if (!PyArray_Check(PyList_GetItem($input,1))) $1 = 0; if (!PyArray_Check(PyList_GetItem($input,2))) $1 = 0; if (!PyArray_Check(PyList_GetItem($input,3))) $1 = 0; - } else $1 = 0; + } else $1 = 0; } } @@ -169,7 +169,7 @@ bool is_HYPRE_USING_CUDA(){ #ifdef HYPRE_BIGINT typedef long long int HYPRE_Int; #define HYPRE_MPI_INT MPI_LONG_LONG_INT -#else +#else typedef int HYPRE_Int; #define HYPRE_MPI_INT MPI_INT #endif @@ -178,13 +178,13 @@ typedef int HYPRE_Int; %pythonprepend mfem::HypreParVector::HypreParVector %{ import numpy as np -self._linked_array = None +self._linked_array = None if isinstance(args[-1], list): v = np.ascontiguousarray(args[-1][0]) col = np.ascontiguousarray(args[-1][1]) args = list(args[:-1]) args.append([v, col]) -%} +%} %pythonappend mfem::HypreParVector::HypreParVector %{ if isinstance(args[-1], list): # in this case, ParVector does not own the object @@ -218,11 +218,11 @@ def parvec__del__(self): self._linked_array = None def parmat__repr__(self): shape = (self.GetGlobalNumRows(), self.GetGlobalNumCols()) - lshape = (self.GetNumRows(), self.GetNumCols()) + lshape = (self.GetNumRows(), self.GetNumCols()) return "HypreParMatrix "+str(shape)+"["+str(lshape)+"]" HypreParVector.__repr__ = parvec__repr__ -HypreParVector.__del__ = parvec__del__ +HypreParVector.__del__ = parvec__del__ HypreParMatrix.__repr__ = parmat__repr__ # setter/getter of _hyperread_called @@ -232,10 +232,10 @@ def hypreread_called(self): return self._xhypreread_called def hypreread_called_setter(self, x): self._xhypreread_called = x - + HypreParVector._hypreread_called = property(hypreread_called).setter(hypreread_called_setter) %} - + %extend mfem::HypreParVector { PyObject* GetPartitioningArray() { @@ -243,7 +243,7 @@ PyObject* GetPartitioningArray() npy_intp dims[] = {2}; int typenum = (sizeof(HYPRE_BigInt) == 4) ? NPY_INT32 : NPY_INT64; HYPRE_BigInt *part_out; - + HYPRE_BigInt *part = self -> Partitioning(); PyObject *tmp_arr = PyArray_ZEROS(1, dims, typenum, 0); PyObject *arr1 = (PyObject *)PyArray_GETCONTIGUOUS((PyArrayObject *)tmp_arr); @@ -252,11 +252,11 @@ PyObject* GetPartitioningArray() part_out = (HYPRE_BigInt *) PyArray_DATA(reinterpret_cast(arr1)); part_out[0] = part[0]; part_out[1] = part[1]; - //part_out[2] = part[2]; + //part_out[2] = part[2]; return arr1; } -} +} %extend mfem::HypreParMatrix { PyObject* GetRowPartArray() { @@ -264,7 +264,7 @@ PyObject* GetRowPartArray() npy_intp dims[] = {2}; int typenum = (sizeof(HYPRE_BigInt) == 4) ? NPY_INT32 : NPY_INT64; HYPRE_BigInt *part_out; - + HYPRE_BigInt *part = self -> RowPart(); PyObject *tmp_arr = PyArray_ZEROS(1, dims, typenum, 0); PyObject *arr1 = (PyObject *)PyArray_GETCONTIGUOUS((PyArrayObject *)tmp_arr); @@ -273,7 +273,7 @@ PyObject* GetRowPartArray() part_out = (HYPRE_BigInt *) PyArray_DATA(reinterpret_cast(arr1)); part_out[0] = part[0]; part_out[1] = part[1]; - //part_out[2] = part[2]; + //part_out[2] = part[2]; return arr1; } @@ -283,7 +283,7 @@ PyObject* GetColPartArray() npy_intp dims[] = {2}; int typenum = (sizeof(HYPRE_BigInt) == 4) ? NPY_INT32 : NPY_INT64; HYPRE_BigInt *part_out; - + HYPRE_BigInt *part = self -> ColPart(); PyObject *tmp_arr = PyArray_ZEROS(1, dims, typenum, 0); PyObject *arr1 = (PyObject *)PyArray_GETCONTIGUOUS((PyArrayObject *)tmp_arr); @@ -292,7 +292,7 @@ PyObject* GetColPartArray() part_out = (HYPRE_BigInt *) PyArray_DATA(reinterpret_cast(arr1)); part_out[0] = part[0]; part_out[1] = part[1]; - //part_out[2] = part[2]; + //part_out[2] = part[2]; return arr1; } @@ -309,25 +309,25 @@ HYPRE_Int get_local_nnz()//mfem::HypreParMatrix *pmatrix) //comm = hypre_ParCSRMatrixComm(matrix); hypre_CSRMatrix *diag = hypre_ParCSRMatrixDiag(matrix); hypre_CSRMatrix *offd = hypre_ParCSRMatrixOffd(matrix); - + const int diag_nnz = mfem::internal::to_int(diag->num_nonzeros); - const int offd_nnz = mfem::internal::to_int(offd->num_nonzeros); + const int offd_nnz = mfem::internal::to_int(offd->num_nonzeros); return (HYPRE_Int)(diag_nnz + offd_nnz); } PyObject* get_local_true_nnz() { hypre_ParCSRMatrix *matrix = static_cast(*self); - + mfem::SparseMatrix merged; self -> MergeDiagAndOffd(merged); - + int * I = merged.GetI(); - int * J = merged.GetJ(); + int * J = merged.GetJ(); double *Data = merged.GetData(); HYPRE_BigInt nnz = merged.NumNonZeroElems(); HYPRE_BigInt tnnz = 0; - + for (int k = 0; k(*self); if (!matrix) { - return Py_None; + return Py_None; } HYPRE_Int myid; MPI_Comm comm = hypre_ParCSRMatrixComm(matrix); hypre_MPI_Comm_rank(comm, &myid); - + hypre_CSRMatrix *diag = hypre_ParCSRMatrixDiag(matrix); hypre_CSRMatrix *offd = hypre_ParCSRMatrixOffd(matrix); const int diag_nnz = mfem::internal::to_int(diag->num_nonzeros); - const int offd_nnz = mfem::internal::to_int(offd->num_nonzeros); - + const int offd_nnz = mfem::internal::to_int(offd->num_nonzeros); + HYPRE_Int first_row_index; HYPRE_Int first_col_diag; first_row_index = hypre_ParCSRMatrixFirstRowIndex(matrix); @@ -370,21 +370,21 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, mfem::SparseMatrix merged; self -> MergeDiagAndOffd(merged); - + HYPRE_BigInt *cpart = self -> ColPart(); HYPRE_BigInt *rpart = self -> RowPart(); int num_rows = self -> Height(); int * I = merged.GetI(); - int * J = merged.GetJ(); + int * J = merged.GetJ(); double *Data = merged.GetData(); - HYPRE_BigInt tnnz = 0; + HYPRE_BigInt tnnz = 0; for (int k = 0; k (arr1)); jcn = (HYPRE_Int *) PyArray_DATA(reinterpret_cast (arr2)); a = (double *) PyArray_DATA(reinterpret_cast (arr3)); @@ -419,7 +419,7 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, ii = first_row_index + i + base_i; for (int j = I[i]; j < I[i+1]; j++) { jj = J[j] + base_j; - if ((double)Data[j] != 0.){ + if ((double)Data[j] != 0.){ irn[innz]= ii; jcn[innz] = jj; a[innz] = (double)Data[j]; @@ -427,8 +427,8 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, } } } - - HYPRE_Int ilower, iupper, jlower, jupper; + + HYPRE_Int ilower, iupper, jlower, jupper; //#ifdef HYPRE_NO_GLOBAL_PARTITION if (HYPRE_AssumedPartitionCheck()){ //std::cout << "no_global_partition\n"; @@ -448,23 +448,23 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, PyList_SetItem(o, 1, PyLong_FromLong((long)ilower)); PyList_SetItem(o, 2, PyLong_FromLong((long)iupper)); PyList_SetItem(o, 3, PyLong_FromLong((long)jlower)); - PyList_SetItem(o, 4, PyLong_FromLong((long)jupper)); + PyList_SetItem(o, 4, PyLong_FromLong((long)jupper)); PyList_SetItem(o, 5, arr1); PyList_SetItem(o, 6, arr2); PyList_SetItem(o, 7, arr3); - + return o; alloc_fail: Py_XDECREF(arr1); Py_XDECREF(arr2); Py_XDECREF(arr3); - Py_XDECREF(o); + Py_XDECREF(o); return Py_None; - - /* + + /* //hypre_ParCSRMatrix *matrix = static_cast(*pmatrix); hypre_ParCSRMatrix *matrix = static_cast(*self); @@ -487,14 +487,14 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, HYPRE_Int myid, num_procs, i, j, I, J; HYPRE_Int num_nonzeros_offd; - + HYPRE_Int innz = 0; HYPRE_Int nnz; - PyObject *arr1 = NULL, *arr2 = NULL, *arr3 = NULL, *o = NULL; + PyObject *arr1 = NULL, *arr2 = NULL, *arr3 = NULL, *o = NULL; if (!matrix) { - return Py_None; + return Py_None; } comm = hypre_ParCSRMatrixComm(matrix); @@ -535,7 +535,7 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, jlower = col_starts[myid] +base_j; jupper = col_starts[myid+1]+base_j - 1; } - + HYPRE_Int tnnz; tnnz = 0; for (i = 0; i < num_rows; i++) @@ -545,10 +545,10 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, if ( diag_data ) { if ((double)diag_data[j] != 0){ - tnnz = tnnz + 1; + tnnz = tnnz + 1; } - } - + } + } if ( num_nonzeros_offd ) { @@ -557,13 +557,13 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, if ( offd_data ) { if ((double)offd_data[j] != 0){ - tnnz = tnnz + 1; + tnnz = tnnz + 1; } } } } } - + HYPRE_Int* irn; HYPRE_Int* jcn; double* a; @@ -584,7 +584,7 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, Py_XDECREF(tmp_arr1); Py_XDECREF(tmp_arr2); Py_XDECREF(tmp_arr3); - + if (arr1 == NULL) goto alloc_fail; if (arr2 == NULL) goto alloc_fail; if (arr3 == NULL) goto alloc_fail; @@ -609,8 +609,8 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, a[innz] = (double)diag_data[j]; innz = innz + 1; } - } - + } + } if ( num_nonzeros_offd ) { @@ -619,7 +619,7 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, J = col_map_offd[offd_j[j]] + base_j; if ( offd_data ) { - if ((double)offd_data[j] != 0.){ + if ((double)offd_data[j] != 0.){ irn[innz]= I;; jcn[innz] = J; a[innz] = (double)offd_data[j]; @@ -635,21 +635,21 @@ PyObject* GetCooDataArray(const HYPRE_Int base_i = 0, PyList_SetItem(o, 1, PyLong_FromLong((long)ilower)); PyList_SetItem(o, 2, PyLong_FromLong((long)iupper)); PyList_SetItem(o, 3, PyLong_FromLong((long)jlower)); - PyList_SetItem(o, 4, PyLong_FromLong((long)jupper)); + PyList_SetItem(o, 4, PyLong_FromLong((long)jupper)); PyList_SetItem(o, 5, arr1); PyList_SetItem(o, 6, arr2); PyList_SetItem(o, 7, arr3); - + return o; alloc_fail: Py_XDECREF(arr1); Py_XDECREF(arr2); Py_XDECREF(arr3); - Py_XDECREF(o); + Py_XDECREF(o); return Py_None; */ } -} +} /* void PrintCommPkg(std::ostream &out = mfem::out) const; diff --git a/mfem/_par/intrules.i b/mfem/_par/intrules.i index abbc4666..709f1f86 100644 --- a/mfem/_par/intrules.i +++ b/mfem/_par/intrules.i @@ -3,6 +3,7 @@ %{ #include "fem/intrules.hpp" #include "numpy/arrayobject.h" +#include "../common/pyintrules.hpp" %} %init %{ @@ -35,3 +36,7 @@ INSTANTIATE_ARRAY0(IntegrationRule *, IntegrationRule, 1) %include "fem/intrules.hpp" +%feature("director") mfem::PyIntegrationRule; +%include "../common/pyintrules.hpp" + + diff --git a/mfem/_par/intrules_cut.i b/mfem/_par/intrules_cut.i new file mode 100644 index 00000000..57ae12e4 --- /dev/null +++ b/mfem/_par/intrules_cut.i @@ -0,0 +1,23 @@ +%module (package="mfem._par", director="1") intrules_cut + +%{ +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +%} + +%init %{ +import_array(); +%} + +%include "exception.i" +%import "../common/exception.i" +%import "array.i" +%import "../common/numpy_int_typemap.i" +%import "mem_manager.i" + +%import "coefficient.i" + +%include "fem/intrules_cut.hpp" diff --git a/mfem/_par/io_stream.i b/mfem/_par/io_stream.i index e6532bb2..ee11c64c 100644 --- a/mfem/_par/io_stream.i +++ b/mfem/_par/io_stream.i @@ -6,7 +6,7 @@ #include "fstream" #include "iostream" #include "string" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" %} %include "../common/io_stream.hpp" diff --git a/mfem/_par/istream_typemap.i b/mfem/_par/istream_typemap.i index 38bd9ab5..cb2b68b5 100644 --- a/mfem/_par/istream_typemap.i +++ b/mfem/_par/istream_typemap.i @@ -4,7 +4,7 @@ %typemap(in) std::istream& (boost_ifdstream *stream=NULL) { FILE *f=PyFile_AsFile($input); // Verify that this returns NULL for non-files if (!f) { - SWIG_Error(SWIG_TypeError, "File object expected."); + SWIG_Error(SWIG_TypeError, "File object expected."); SWIG_fail; } else { diff --git a/mfem/_par/linearform.i b/mfem/_par/linearform.i index f5c24907..3addabcb 100644 --- a/mfem/_par/linearform.i +++ b/mfem/_par/linearform.i @@ -1,12 +1,5 @@ %module(package="mfem._par", directors="1") linearform %{ -#include "fem/fem.hpp" -#include "fem/fe_coll.hpp" -#include "fem/fespace.hpp" -#include "fem/eltrans.hpp" -#include "fem/coefficient.hpp" -#include "fem/linearform.hpp" -#include "fem/intrules.hpp" #include #include #include @@ -14,9 +7,12 @@ #include #include #include +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pylininteg.hpp" %} %init %{ @@ -40,33 +36,33 @@ import_array(); %exception { try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } + catch (Swig::DirectorException &e) { SWIG_fail; } } //%include "fem/coefficient.hpp" -namespace mfem { -%pythonprepend LinearForm::AddDomainIntegrator %{ +namespace mfem { +%pythonprepend LinearForm::AddDomainIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - lfi = args[0] + lfi = args[0] self._integrators.append(lfi) - lfi.thisown=0 + lfi.thisown=0 %} -%pythonprepend LinearForm::AddBoundaryIntegrator %{ +%pythonprepend LinearForm::AddBoundaryIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - lfi = args[0] + lfi = args[0] self._integrators.append(lfi) - lfi.thisown=0 - %} -%pythonprepend LinearForm::AddBdrFaceIntegrator %{ + lfi.thisown=0 + %} +%pythonprepend LinearForm::AddBdrFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - lfi = args[0] + lfi = args[0] self._integrators.append(lfi) - lfi.thisown=0 - %} + lfi.thisown=0 + %} %pythonprepend LinearForm::AddInteriorFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(lfi) - lfi.thisown=0 + lfi.thisown=0 %} } %include "fem/linearform.hpp" diff --git a/mfem/_par/lininteg.i b/mfem/_par/lininteg.i index f9fa5def..facf8c0c 100644 --- a/mfem/_par/lininteg.i +++ b/mfem/_par/lininteg.i @@ -7,38 +7,36 @@ #include #include #include -#include "mfem.hpp" -#include "pyoperator.hpp" +#include "mfem.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "../common/pylininteg.hpp" +#include "../common/pyintrules.hpp" +#include "numpy/arrayobject.h" %} %init %{ import_array(); %} - //%include "fem/coefficient.hpp" +%include "exception.i" %import "globals.i" + +//%include "fem/coefficient.hpp" %import "fe.i" %import "vector.i" %import "eltrans.i" %import "intrules.i" %import "coefficient.i" +%import "../common/exception_director.i" %import "fespace.i" - -%exception { - try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } - //catch (...){ - // SWIG_fail; - //} - // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } -} - %include "../common/lininteg_ext.i" %include "fem/lininteg.hpp" +%feature("director") mfem::PyLinearFormIntegrator; +%include "../common/pylininteg.hpp" + + diff --git a/mfem/_par/matrix.i b/mfem/_par/matrix.i index 1fda3f82..56b2871c 100644 --- a/mfem/_par/matrix.i +++ b/mfem/_par/matrix.i @@ -6,9 +6,9 @@ #include #include #include "mfem.hpp" -#include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" %} %begin %{ diff --git a/mfem/_par/mem_manager.i b/mfem/_par/mem_manager.i index d775faad..d6538d00 100644 --- a/mfem/_par/mem_manager.i +++ b/mfem/_par/mem_manager.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/mem_manager.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_par/mesh.i b/mfem/_par/mesh.i index e7aec5d2..9abaead7 100644 --- a/mfem/_par/mesh.i +++ b/mfem/_par/mesh.i @@ -11,9 +11,10 @@ #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" #include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} diff --git a/mfem/_par/mesh_operators.i b/mfem/_par/mesh_operators.i index fc77f2cc..2ca72b04 100644 --- a/mfem/_par/mesh_operators.i +++ b/mfem/_par/mesh_operators.i @@ -3,8 +3,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} // initialization required to return numpy array from SWIG %init %{ @@ -19,5 +20,5 @@ import_array(); %include "../common/typemap_macros.i" LIST_TO_MFEMOBJ_POINTERARRAY_IN(mfem::IntegrationRule const *irs_[], mfem::IntegrationRule *, 1) -%include "mesh/mesh_operators.hpp" +%include "mesh/mesh_operators.hpp" diff --git a/mfem/_par/multigrid.i b/mfem/_par/multigrid.i index 85a481eb..d04b185d 100644 --- a/mfem/_par/multigrid.i +++ b/mfem/_par/multigrid.i @@ -6,12 +6,12 @@ %module(package="mfem._par") multigrid %feature("autodoc", "1"); %{ -#include "linalg/operator.hpp" -#include "linalg/handle.hpp" -#include "fem/multigrid.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ import_array(); @@ -39,30 +39,30 @@ LIST_TO_MFEMOBJ_BOOLARRAY_IN(const mfem::Array& ) %} %pythonprepend mfem::PyGeometricMultigrid::AppendEssentialTDofs %{ if not hasattr(self, "_esss"): self._esss = [] - self._esss.append(ess) + self._esss.append(ess) ess.thisown = 0 %} %feature("shadow") mfem::PyGeometricMultigrid::_pybfs %{ - @property + @property def bfs(self): return self._forms - %} -%feature("shadow") mfem::PyGeometricMultigrid::_pyess %{ - @property + %} +%feature("shadow") mfem::PyGeometricMultigrid::_pyess %{ + @property def essentialTrueDofs(self): return self._esss -%} +%} %include "fem/multigrid.hpp" %inline %{ - namespace mfem{ + namespace mfem{ class PyGeometricMultigrid : public GeometricMultigrid { public: - PyGeometricMultigrid(const FiniteElementSpaceHierarchy& fespaces_) + PyGeometricMultigrid(const FiniteElementSpaceHierarchy& fespaces_) : GeometricMultigrid(fespaces_){} - + void AppendBilinearForm(BilinearForm *form){ bfs.Append(form); } @@ -70,10 +70,10 @@ public: essentialTrueDofs.Append(ess); } void _pybfs(void){} - void _pyess(void){} + void _pyess(void){} }; - } /* end of namespace */ + } /* end of namespace */ %} - + diff --git a/mfem/_par/ncmesh.i b/mfem/_par/ncmesh.i index d1220008..98404bed 100644 --- a/mfem/_par/ncmesh.i +++ b/mfem/_par/ncmesh.i @@ -6,10 +6,11 @@ #include #include #include "mfem.hpp" -#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/nonlinearform.i b/mfem/_par/nonlinearform.i index 83d70fc9..1f6f4f73 100644 --- a/mfem/_par/nonlinearform.i +++ b/mfem/_par/nonlinearform.i @@ -1,10 +1,13 @@ %module(package="mfem._par") nonlinearform %{ #include -#include "mfem.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pynonlininteg.hpp" %} @@ -20,38 +23,40 @@ import_array(); %import "../common/exception.i" %include "../common/typemap_macros.i" -namespace mfem { +namespace mfem { %pythonprepend NonlinearForm::AddDomainIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] + nlfi = args[0] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend NonlinearForm::AddInteriorFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend NonlinearForm::AddBdrFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] -# self._integrators.append(nlfi) nlfi = args[0] - nlfi.thisown=0 +# self._integrators.append(nlfi) + nlfi.thisown=0 %} %pythonprepend BlockNonlinearForm::AddDomainIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] + nlfi = args[0] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend BlockNonlinearForm::AddInteriorFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend BlockNonlinearForm::AddBdrFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] -# self._integrators.append(nlfi) nlfi = args[0] - nlfi.thisown=0 +# self._integrators.append(nlfi) + nlfi.thisown=0 %} } diff --git a/mfem/_par/nonlininteg.i b/mfem/_par/nonlininteg.i index 1b1c27d9..240cbbd6 100644 --- a/mfem/_par/nonlininteg.i +++ b/mfem/_par/nonlininteg.i @@ -1,9 +1,11 @@ %module(package="mfem._par", directors="1") nonlininteg %{ -#include "mfem.hpp" +#include "mfem.hpp" #include "../common/pycoefficient.hpp" -#include "pyoperator.hpp" -using namespace mfem; +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pynonlininteg.hpp" +using namespace mfem; %} /* %init %{ @@ -11,26 +13,15 @@ import_array(); %} */ -%exception { - try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } - //catch (...){ - // SWIG_fail; - //} - // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } -} -%feature("director:except") { - if ($error != NULL) { - throw Swig::DirectorMethodException(); - } -} - +%include "exception.i" %import vector.i %import operators.i %import fespace.i %import eltrans.i - -%feature("director") mfem::NonlinearFormIntegrator; +%import "../common/exception_director.i" %include "fem/nonlininteg.hpp" + +%feature("director") mfem::PyNonlinearFormIntegrator; +%include "../common/pynonlininteg.hpp" + diff --git a/mfem/_par/ode.i b/mfem/_par/ode.i index b0c9afb5..33538fc7 100644 --- a/mfem/_par/ode.i +++ b/mfem/_par/ode.i @@ -2,8 +2,8 @@ %{ #include "mfem.hpp" #include "linalg/ode.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" %} diff --git a/mfem/_par/operators.i b/mfem/_par/operators.i index b931cc46..59678351 100644 --- a/mfem/_par/operators.i +++ b/mfem/_par/operators.i @@ -6,9 +6,9 @@ #include #include #include "mfem.hpp" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} %init %{ @@ -26,12 +26,12 @@ OSTREAM_TYPEMAP(std::ostream&) %exception { try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } + catch (Swig::DirectorException &e) { SWIG_fail; } //catch (...){ // SWIG_fail; //} // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } + // catch (std::exception &e) { SWIG_fail; } } %feature("director:except") { if ($error != NULL) { @@ -83,7 +83,7 @@ IGNORE_ARRAY_METHODS(mfem::Solver *) INSTANTIATE_ARRAY0(Solver *, Solver, 1) %include "linalg/operator.hpp" -%include "pyoperator.hpp" +%include "../common/pyoperator.hpp" %pythoncode %{ class PyOperator(PyOperatorBase): @@ -95,13 +95,13 @@ class PyOperator(PyOperatorBase): raise NotImplementedError('you must specify this method') class PyTimeDependentOperator(PyTimeDependentOperatorBase): - def __init__(self, *args): + def __init__(self, *args): PyTimeDependentOperatorBase.__init__(self, *args) def _EvalMult(self, x): return self.EvalMult(x.GetDataArray()) def EvalMult(self, x): raise NotImplementedError('you must specify this method') - + %} /* diff --git a/mfem/_par/ostream_typemap.i b/mfem/_par/ostream_typemap.i index 7d6ce7be..fdd7940c 100644 --- a/mfem/_par/ostream_typemap.i +++ b/mfem/_par/ostream_typemap.i @@ -35,7 +35,7 @@ SWIG_fail; } else { - std::ofstream out(filename); + std::ofstream out(filename); $1 = &out; } } diff --git a/mfem/_par/pbilinearform.i b/mfem/_par/pbilinearform.i index ea315275..8a04358b 100644 --- a/mfem/_par/pbilinearform.i +++ b/mfem/_par/pbilinearform.i @@ -1,11 +1,11 @@ %module(package="mfem._par") pbilinearform %{ - //#include -#include "config/config.hpp" -#include "fem/pbilinearform.hpp" +//#include +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" @@ -38,14 +38,37 @@ import_array(); mfem::Vector &x, mfem::Vector &b, OpType &A, mfem::Vector &X, mfem::Vector &B, int copy_interior = 0){ - return self->mfem::BilinearForm::FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior); + return self->mfem::BilinearForm::FormLinearSystem(ess_tdof_list, + x, b, A, X, B, + copy_interior); } template void FormSystemMatrix(const mfem::Array &ess_tdof_list, OpType &A){ return self->mfem::BilinearForm::FormSystemMatrix(ess_tdof_list, A); } -}; +}; +%extend mfem::ParMixedBilinearForm { + template + void FormRectangularSystemMatrix(const Array &trial_tdof_list, + const Array &test_tdof_list, OpType &A){ + return self->mfem::MixedBilinearForm::FormRectangularSystemMatrix(trial_tdof_list, + test_tdof_list, + A); + } + + template + void FormRectangularLinearSystem(const Array &trial_tdof_list, + const Array &test_tdof_list, + Vector &x, Vector &b, + OpType &A, Vector &X, Vector &B){ + return self->mfem::MixedBilinearForm::FormRectangularLinearSystem(trial_tdof_list, + test_tdof_list, + x, b, + A, + X, B); + } +}; // instatitate template methods @@ -54,15 +77,17 @@ import_array(); %define P_FORM_SYSTEM_MATRIX_WRAP(OsType) %template(FormLinearSystem) mfem::ParBilinearForm::FormLinearSystem; %template(FormSystemMatrix) mfem::ParBilinearForm::FormSystemMatrix; +%template(FormRectangularLinearSystem) mfem::ParMixedBilinearForm::FormRectangularLinearSystem; +%template(FormRectangularSystemMatrix) mfem::ParMixedBilinearForm::FormRectangularSystemMatrix; %enddef P_FORM_SYSTEM_MATRIX_WRAP(mfem::SparseMatrix) - + #ifdef MFEM_USE_MPI P_FORM_SYSTEM_MATRIX_WRAP(mfem::HypreParMatrix) #endif - + #ifdef MFEM_USE_PETSC P_FORM_SYSTEM_MATRIX_WRAP(mfem::PetscParMatrix) -#endif +#endif diff --git a/mfem/_par/pfespace.i b/mfem/_par/pfespace.i index cedd86d9..b3a1331c 100644 --- a/mfem/_par/pfespace.i +++ b/mfem/_par/pfespace.i @@ -1,14 +1,11 @@ %module(package="mfem._par") pfespace %{ #include -#include "config/config.hpp" -#include "fem/linearform.hpp" -#include "fem/pfespace.hpp" -#include "fem/restriction.hpp" -#include "fem/prestriction.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" @@ -45,7 +42,7 @@ import_array(); %feature("shadow") mfem::ParFiniteElementSpace::GetSharedEdgeDofs %{ def GetSharedEdgeDofs(self, group, ei): from .array import intArray - dofs = intArray() + dofs = intArray() $action(self, group, ei, dofs) return dofs.ToList() %} @@ -90,7 +87,7 @@ def GetFaceNbrElementVDofs(self, i): return self->GetBdrElementDofs(bel, dofs); } virtual DofTransformation *GetFaceNbrVDofTransformation(int elem) const { - mfem::Array dofs; + mfem::Array dofs; return self->GetFaceNbrElementVDofs(elem, dofs); } }; diff --git a/mfem/_par/pgridfunc.i b/mfem/_par/pgridfunc.i index 115bf2a5..515c2751 100644 --- a/mfem/_par/pgridfunc.i +++ b/mfem/_par/pgridfunc.i @@ -8,13 +8,15 @@ #include #include #include -#include +#include #include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" -#include "../common/pycoefficient.hpp" #include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %include "../common/mfem_config.i" @@ -50,12 +52,12 @@ ISTREAM_TYPEMAP(std::istream&) $1 = (mfem::IntegrationRule **) malloc((size)*sizeof(mfem::IntegrationRule *)); for (i = 0; i < size; i++) { PyObject *o = PyList_GetItem($input,i); - void *temp; + void *temp; if (SWIG_ConvertPtr(o, &temp, $descriptor(mfem::IntegrationRule *),SWIG_POINTER_EXCEPTION) == -1){ return NULL; } - $1[i] = reinterpret_cast(temp); + $1[i] = reinterpret_cast(temp); } } else { PyErr_SetString(PyExc_TypeError,"not a list"); @@ -72,6 +74,7 @@ ISTREAM_TYPEMAP(std::istream&) %newobject mfem::ParGridFunction::ParallelAverage; %newobject mfem::ParGridFunction::ParallelProject; %newobject mfem::ParGridFunction::GetTrueDofs; +%newobject mfem::ParGridFunction::GetSerialGridFunction; %pythonprepend mfem::ParGridFunction::ParGridFunction %{ @@ -90,18 +93,24 @@ if (len(args) == 2 and isinstance(args[1], str) and pfes.thisown = 0 g0.thisown = 0 self.this = x.this - return + return %} - + %include "../common/typemap_macros.i" LIST_TO_MFEMOBJ_POINTERARRAY_IN(mfem::IntegrationRule const *irs[], mfem::IntegrationRule *, 0) +%typemap(out, optimal="1") mfem::GridFunction %{ + /* return by value optimization */ + $result = SWIG_NewPointerObj(SWIG_as_voidptr(new $1_ltype($1)), $descriptor(mfem::GridFunction *), 1); +%} + +%exception; /* undo default director exception */ %include "fem/pgridfunc.hpp" namespace mfem{ %extend ParGridFunction{ ParGridFunction(mfem::ParFiniteElementSpace *fes, const mfem::Vector &v, int offset){ - mfem::ParGridFunction *gf; + mfem::ParGridFunction *gf; gf = new mfem::ParGridFunction(fes, v.GetData() + offset); return gf; } @@ -119,12 +128,12 @@ ParGridFunction(mfem::ParFiniteElementSpace *fes, const mfem::Vector &v, int off } //void Assign(const mfem::GridFunction &v) { // (* self) = v; - //} + //} void Assign(PyObject* param) { /* note that these error does not raise error in python type check is actually done in wrapper layer */ PyArrayObject *param0 = reinterpret_cast(param); - + if (!PyArray_Check(param0)){ PyErr_SetString(PyExc_ValueError, "Input data must be ndarray"); return; @@ -139,19 +148,19 @@ ParGridFunction(mfem::ParFiniteElementSpace *fes, const mfem::Vector &v, int off PyErr_SetString(PyExc_ValueError, "Input data NDIM must be one"); return ; } - npy_intp *shape = PyArray_DIMS(param0); + npy_intp *shape = PyArray_DIMS(param0); int len = self->Size(); - if (shape[0] != len){ + if (shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; - } + } (mfem::Vector &)(* self) = (double *) PyArray_DATA(param0); } - + /* this will be turn on in mfem-3.3.3 ParGridFunction(ParMesh *pmesh, const char *gf_file){ mfem::ParGridFunction *pgf; - mfem::ParFiniteElementSpace *pfes; + mfem::ParFiniteElementSpace *pfes; std::ifstream gfstream(gf_file); if (!gfstream) { @@ -161,9 +170,9 @@ ParGridFunction(ParMesh *pmesh, const char *gf_file){ pgf = new mfem::GridFunction(pmesh, gfstream); return pgf; } -*/ +*/ }; //end of extend -} // end of namespace +} // end of namespace /* virtual void Save(std::ostream &out) const; diff --git a/mfem/_par/plinearform.i b/mfem/_par/plinearform.i index 34ec30b1..4f50dfff 100644 --- a/mfem/_par/plinearform.i +++ b/mfem/_par/plinearform.i @@ -1,9 +1,10 @@ %module(package="mfem._par") plinearform %{ #include "mfem.hpp" -#include "pyoperator.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/pmesh.i b/mfem/_par/pmesh.i index dbb346e8..b7b6cf7a 100644 --- a/mfem/_par/pmesh.i +++ b/mfem/_par/pmesh.i @@ -8,13 +8,14 @@ #include #include #include -#include +#include #include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/io_stream.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" @@ -50,33 +51,38 @@ ISTREAM_TYPEMAP(std::istream&) %feature("shadow") mfem::ParMesh::GroupFace %{ def GroupFace(self, group, i, *args): if len(args) == 0: - from mfem.par import intp + from mfem.par import intp face = intp() o = intp() - $action(self, group, i, face, o) + $action(self, group, i, face, o) return face.value(), o.value() else: - return $action(self, group, i, *args) + return $action(self, group, i, *args) %} - + %feature("shadow") mfem::ParMesh::GroupEdge %{ def GroupEdge(self, group, i, *args): if len(args) == 0: - from mfem.par import intp + from mfem.par import intp edge = intp() - o = intp() + o = intp() $action(self, group, i, edge, o) return edge.value(), o.value() else: - return $action(self, group, i, *args) + return $action(self, group, i, *args) %} +%typemap(out, optimal="1") mfem::Mesh %{ + /* return by value optimization */ + $result = SWIG_NewPointerObj(SWIG_as_voidptr(new $1_ltype($1)), $descriptor(mfem::Mesh *), 1); +%} +%exception; /* undo default director exception */ %include "mesh/pmesh.hpp" namespace mfem{ %extend ParMesh{ - // + // //ParMesh(MPI_Comm comm, const char *mesh_file){ //mfem::ParMesh *mesh; //std::ifstream imesh(mesh_file); @@ -90,11 +96,11 @@ namespace mfem{ //} void ParPrintToFile(const char *mesh_file, const int precision) const { - std::ofstream mesh_ofs(mesh_file); + std::ofstream mesh_ofs(mesh_file); mesh_ofs.precision(precision); - self->ParPrint(mesh_ofs); + self->ParPrint(mesh_ofs); } -}; +}; } /* diff --git a/mfem/_par/pncmesh.i b/mfem/_par/pncmesh.i index bcedd4f9..a8886915 100644 --- a/mfem/_par/pncmesh.i +++ b/mfem/_par/pncmesh.i @@ -4,13 +4,13 @@ %{ #include -#include "../common/io_stream.hpp" -#include "config/config.hpp" -#include "mesh/mesh_headers.hpp" #include "mpi4py/mpi4py.h" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/pnonlinearform.i b/mfem/_par/pnonlinearform.i index 57ab7060..c0db54ec 100644 --- a/mfem/_par/pnonlinearform.i +++ b/mfem/_par/pnonlinearform.i @@ -1,12 +1,11 @@ %module(package="mfem._par") pnonlinearform %{ #include -#include "config/config.hpp" -#include "fem/pnonlinearform.hpp" -#include "fem/linearform.hpp" -#include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/point.i b/mfem/_par/point.i index 78f3c118..26aca69b 100644 --- a/mfem/_par/point.i +++ b/mfem/_par/point.i @@ -4,8 +4,9 @@ %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/prestriction.i b/mfem/_par/prestriction.i index 55de03fd..959f2aed 100644 --- a/mfem/_par/prestriction.i +++ b/mfem/_par/prestriction.i @@ -1,10 +1,11 @@ %module(package="mfem._par") prestriction %{ #include "mfem.hpp" -#include "fem/prestriction.hpp" +#include "fem/prestriction.hpp" // note:prestrition.hpp is not inclured from mfem.hpp #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/psubmesh.i b/mfem/_par/psubmesh.i index c7d57819..440766b1 100644 --- a/mfem/_par/psubmesh.i +++ b/mfem/_par/psubmesh.i @@ -5,8 +5,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/ptransfermap.i b/mfem/_par/ptransfermap.i index 5d051ded..491b5fcf 100644 --- a/mfem/_par/ptransfermap.i +++ b/mfem/_par/ptransfermap.i @@ -5,8 +5,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/pumi.i b/mfem/_par/pumi.i index bff971f5..97210663 100644 --- a/mfem/_par/pumi.i +++ b/mfem/_par/pumi.i @@ -15,7 +15,7 @@ #include #include #include -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" #include "../common/pycoefficient.hpp" diff --git a/mfem/_par/qfunction.i b/mfem/_par/qfunction.i index aef40249..e7fec570 100644 --- a/mfem/_par/qfunction.i +++ b/mfem/_par/qfunction.i @@ -1,10 +1,11 @@ %module(package="mfem._par") qfunction %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/qspace.i b/mfem/_par/qspace.i index ee72ccd3..1de6a752 100644 --- a/mfem/_par/qspace.i +++ b/mfem/_par/qspace.i @@ -1,10 +1,11 @@ %module(package="mfem._par") qspace %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/quadinterpolator.i b/mfem/_par/quadinterpolator.i index 378f0378..383d03f3 100644 --- a/mfem/_par/quadinterpolator.i +++ b/mfem/_par/quadinterpolator.i @@ -1,10 +1,11 @@ %module(package="mfem._par") quadinterpolator %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/quadinterpolator_face.i b/mfem/_par/quadinterpolator_face.i index 9cdc6e22..435c4d9d 100644 --- a/mfem/_par/quadinterpolator_face.i +++ b/mfem/_par/quadinterpolator_face.i @@ -1,10 +1,11 @@ %module(package="mfem._par") quadinterpolator_face %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/quadrilateral.i b/mfem/_par/quadrilateral.i index eab38f52..93b1f7df 100644 --- a/mfem/_par/quadrilateral.i +++ b/mfem/_par/quadrilateral.i @@ -1,8 +1,9 @@ %module(package="mfem._par") quadrilateral %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/restriction.i b/mfem/_par/restriction.i index 50b12d88..3649a3e2 100644 --- a/mfem/_par/restriction.i +++ b/mfem/_par/restriction.i @@ -1,10 +1,10 @@ %module(package="mfem._par") restriction %{ #include "mfem.hpp" -#include "fem/restriction.hpp" -#include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/schwarz.i b/mfem/_par/schwarz.i index c06f02b3..e1ac028f 100644 --- a/mfem/_par/schwarz.i +++ b/mfem/_par/schwarz.i @@ -1,10 +1,10 @@ %module(package="mfem._par") schwarz %{ -#include "mfem.hpp" +#include "mfem.hpp" #include "../../headers/schwarz.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "numpy/arrayobject.h" %} %include "../common/mfem_config.i" diff --git a/mfem/_par/segment.i b/mfem/_par/segment.i index a8500a19..f57d0223 100644 --- a/mfem/_par/segment.i +++ b/mfem/_par/segment.i @@ -1,8 +1,9 @@ %module(package="mfem._par") segment %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/sets.i b/mfem/_par/sets.i index 41a926fc..a9199219 100644 --- a/mfem/_par/sets.i +++ b/mfem/_par/sets.i @@ -2,7 +2,7 @@ %{ #include #include "general/sets.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_par/setup.py b/mfem/_par/setup.py index 6a3fb8d5..d02736b1 100644 --- a/mfem/_par/setup.py +++ b/mfem/_par/setup.py @@ -106,7 +106,8 @@ def get_extensions(): "linearform", "vector", "lininteg", "complex_operator", "complex_fem", "gridfunc", "hybridization", "bilinearform", - "bilininteg", "intrules", "sparsemat", "densemat", + "bilininteg", "intrules", "intrules_cut", + "sparsemat", "densemat", "solvers", "estimators", "mesh_operators", "ode", "sparsesmoothers", "ncmesh", "matrix", "operators", "eltrans", "geom", @@ -119,7 +120,8 @@ def get_extensions(): "transfer", "dist_solver", "std_vectors", "auxiliary", "tmop", "tmop_amr", "tmop_tools", "qspace", "qfunction", "quadinterpolator", "quadinterpolator_face", - "submesh", "transfermap", "psubmesh", "ptransfermap"] + "submesh", "transfermap", "staticcond","sidredatacollection", + "psubmesh", "ptransfermap"] if add_pumi == '1': from setup_local import puminc, pumilib diff --git a/mfem/_par/sidredatacollection.i b/mfem/_par/sidredatacollection.i new file mode 100644 index 00000000..98d39223 --- /dev/null +++ b/mfem/_par/sidredatacollection.i @@ -0,0 +1,17 @@ +%module(package="mfem._par") sidredatacollection +%{ +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +%} + +%init %{ +import_array(); +%} + +%include "exception.i" +%import "datacollection.i" + +%include "fem/sidredatacollection.hpp" diff --git a/mfem/_par/socketstream.i b/mfem/_par/socketstream.i index d64bc8b2..b4a555f5 100644 --- a/mfem/_par/socketstream.i +++ b/mfem/_par/socketstream.i @@ -4,10 +4,11 @@ %{ #include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -26,23 +27,23 @@ import_array(); %extend mfem::socketstream{ int precision(const int p) { - return self->precision(p); + return self->precision(p); } int precision() - { + { return self->precision(); } void send_solution(const mfem::Mesh &mesh, - const mfem::GridFunction &gf) + const mfem::GridFunction &gf) { *self << "solution\n" << mesh << gf << std::flush; } void send_text(const char ostr[]) - { + { *self << ostr << std::endl; } void flush() - { + { self->flush(); } bool good() @@ -50,22 +51,22 @@ import_array(); return self->std::iostream::good(); } mfem::socketstream& __lshift__(const char ostr[]) - { + { *self << ostr; return *self; } mfem::socketstream& __lshift__(const int x) - { + { *self << x; return *self; } mfem::socketstream& __lshift__(const mfem::Mesh &mesh) - { + { *self << mesh; return *self; } mfem::socketstream& __lshift__(const mfem::GridFunction &gf) - { + { *self << gf; return *self; } @@ -73,5 +74,5 @@ import_array(); { *self << std::endl; return *self; - } -} + } +} diff --git a/mfem/_par/solvers.i b/mfem/_par/solvers.i index 25c434fd..49e46c4e 100644 --- a/mfem/_par/solvers.i +++ b/mfem/_par/solvers.i @@ -5,8 +5,8 @@ #include "linalg/matrix.hpp" #include "linalg/sparsemat.hpp" #include "linalg/solvers.hpp" -#include "pyoperator.hpp" -#include "../common/pysolvers.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pysolvers.hpp" #include "numpy/arrayobject.h" using namespace mfem; %} @@ -28,6 +28,7 @@ import_array(); %import "operators.i" %import "matrix.i" %import "sparsemat.i" +%import "hypre.i" %import "../common/exception.i" %ignore mfem::IterativeSolverMonitor::SetIterativeSolver; @@ -69,14 +70,14 @@ namespace mfem{ mfem_error("Mult is not implemented"); } void PyIterativeSolver::MultTranspose(const Vector &b, Vector &x) const{ - mfem_error("MultTranspose is not implemented"); + mfem_error("MultTranspose is not implemented"); } void PyIterativeSolver::SetPreconditioner(Solver &pr){ - mfem_error("SetPreconditioner is not implemented"); + mfem_error("SetPreconditioner is not implemented"); } /// Also calls SetOperator for the preconditioner if there is one void PyIterativeSolver::SetOperator(const Operator &op){ - mfem_error("SetOperator is not implemented"); + mfem_error("SetOperator is not implemented"); } } /* end of namespace */ %} diff --git a/mfem/_par/sort_pairs.i b/mfem/_par/sort_pairs.i index 5bcc8a38..72f30c89 100644 --- a/mfem/_par/sort_pairs.i +++ b/mfem/_par/sort_pairs.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/globals.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_par/sparsemat.i b/mfem/_par/sparsemat.i index 0c7b48fd..ebbd9f56 100644 --- a/mfem/_par/sparsemat.i +++ b/mfem/_par/sparsemat.i @@ -1,14 +1,14 @@ %module (package="mfem._par") sparsemat %{ -#include +#include #include #include #include #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/io_stream.hpp" using namespace mfem; %} @@ -42,11 +42,11 @@ OSTREAM_TYPEMAP(std::ostream&) return self %} %pythonappend mfem::SparseMatrix::operator+= %{ - val.thisown = 0 + val.thisown = 0 return self %} %pythonprepend mfem::SparseMatrix::SparseMatrix %{ -import numpy as np +import numpy as np from scipy.sparse import csr_matrix if len(args) == 1 and isinstance(args[0], csr_matrix): csr = args[0] @@ -66,9 +66,9 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): self._i_data = i self._j_data = j self._d_data = data - + return -%} +%} // RAP_P, RAP_R replaces RAP, since RAP has two definition one accept // pointer and the other accept reference. From Python, two @@ -78,8 +78,8 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): const mfem::SparseMatrix &R, mfem::SparseMatrix *ORAP){ return RAP(A, R, ORAP); - } - + } + mfem::SparseMatrix *RAP_R(const mfem::SparseMatrix &Rt, const mfem::SparseMatrix &A, const mfem::SparseMatrix &P){ @@ -88,15 +88,15 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): mfem::SparseMatrix &OperatorPtr2SparseMatrix(mfem::OperatorPtr op) { return dynamic_cast(* op); } - + mfem::SparseMatrix &OperatorHandle2SparseMatrix(mfem::OperatorHandle op) { return dynamic_cast(* op); } - + %} /* - support numpy array input to + support numpy array input to SparseMatrix(int *i, int *j, double *data, int m, int n); allows to use numpy array to call this */ @@ -119,11 +119,11 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): //PyArray_CLEARFLAGS(tmp_arr1_, NPY_ARRAY_OWNDATA); //PyArray_CLEARFLAGS(tmp_arr2_, NPY_ARRAY_OWNDATA); // - PyArray_CLEARFLAGS(tmp_arr3_, NPY_ARRAY_OWNDATA); + PyArray_CLEARFLAGS(tmp_arr3_, NPY_ARRAY_OWNDATA); } %typemap(freearg) (int *i, int *j, double *data, int m, int n){ //Py_XDECREF(tmp_arr1_$argnum); Dont do this.. We set OwnsGraph and OwnsData to Fase in Python - //Py_XDECREF(tmp_arr2_$argnum); + //Py_XDECREF(tmp_arr2_$argnum); //Py_XDECREF(tmp_arr3_$argnum); } @@ -138,7 +138,7 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): if (!PyArray_Check(PyList_GetItem($input,2))) $1 = 0; if (!PyInt_Check(PyList_GetItem($input,3))) $1 = 0; if (!PyInt_Check(PyList_GetItem($input,4))) $1 = 0; - } else $1 = 0; + } else $1 = 0; } } @@ -162,7 +162,7 @@ PyObject* GetJArray(void) const{ } PyObject* GetDataArray(void) const{ const int * I = self->GetI(); - const double * A = self->GetData(); + const double * A = self->GetData(); int L = self->Size(); npy_intp dims[] = {I[L]}; return PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, (void *)A); diff --git a/mfem/_par/sparsesmoothers.i b/mfem/_par/sparsesmoothers.i index b554136b..40c71fda 100644 --- a/mfem/_par/sparsesmoothers.i +++ b/mfem/_par/sparsesmoothers.i @@ -1,8 +1,8 @@ %module(package="mfem._par") sparsesmoothers %{ #include "linalg/sparsesmoothers.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "numpy/arrayobject.h" %} %init %{ @@ -16,4 +16,4 @@ import_array(); %import "matrix.i" %import "../common/exception.i" -%include "linalg/sparsesmoothers.hpp" +%include "linalg/sparsesmoothers.hpp" diff --git a/mfem/_par/stable3d.i b/mfem/_par/stable3d.i index 25244808..b45783a0 100644 --- a/mfem/_par/stable3d.i +++ b/mfem/_par/stable3d.i @@ -4,10 +4,11 @@ %{ #include -#include "mfem.hpp" +#include "mfem.hpp" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %begin %{ diff --git a/mfem/_par/staticcond.i b/mfem/_par/staticcond.i new file mode 100644 index 00000000..ea2e5133 --- /dev/null +++ b/mfem/_par/staticcond.i @@ -0,0 +1,18 @@ +%module(package="mfem._par") staticcond +%{ +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +%} + +%init %{ +import_array(); +%} + +%include "exception.i" +%import "fespace.i" +%import "pfespace.i" + +%include "fem/staticcond.hpp" diff --git a/mfem/_par/std_vectors.i b/mfem/_par/std_vectors.i index b83a1c1b..27243250 100644 --- a/mfem/_par/std_vectors.i +++ b/mfem/_par/std_vectors.i @@ -7,9 +7,9 @@ // in a module which imports i file where std_vector.i is imported. %{ #include -#include "mfem.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" #include "../common/io_stream.hpp" %} @@ -35,4 +35,4 @@ import_array(); %template(vector_HypreParMatrix) std::vector; - + diff --git a/mfem/_par/strumpack.i b/mfem/_par/strumpack.i index d432a19c..32dfd121 100644 --- a/mfem/_par/strumpack.i +++ b/mfem/_par/strumpack.i @@ -13,10 +13,10 @@ #include #include #include -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" #include "../common/pycoefficient.hpp" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} @@ -100,7 +100,7 @@ char **argv_obj(PyObject* input){ %pythonprepend mfem::STRUMPACKSolver::STRUMPACKSolver %{ attach_argv = False if isinstance(args[0], list): - aa = [""]+args[0] + aa = [""]+args[0] num = len(aa) ptr = argv_obj(aa) args = (num, ptr, args[1]) @@ -111,7 +111,7 @@ char **argv_obj(PyObject* input){ %pythonappend mfem::STRUMPACKSolver::STRUMPACKSolver %{ if attach_argv: self._argv = ptr -%} +%} %include "SPOptions.hpp" %include "linalg/strumpack.hpp" diff --git a/mfem/_par/submesh.i b/mfem/_par/submesh.i index f27716b1..a26ad6a0 100644 --- a/mfem/_par/submesh.i +++ b/mfem/_par/submesh.i @@ -5,8 +5,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/symmat.i b/mfem/_par/symmat.i index 6ad3a8b0..2a56ebe2 100644 --- a/mfem/_par/symmat.i +++ b/mfem/_par/symmat.i @@ -3,8 +3,8 @@ #include "mfem.hpp" #include "linalg/symmat.hpp" #include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" %} %init %{ diff --git a/mfem/_par/table.i b/mfem/_par/table.i index 94e4b045..6934db04 100644 --- a/mfem/_par/table.i +++ b/mfem/_par/table.i @@ -3,10 +3,10 @@ %feature("autodoc", "1"); %{ -#include +#include #include -#include "mfem.hpp" -#include "numpy/arrayobject.h" +#include "mfem.hpp" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" #include "general/table.hpp" %} diff --git a/mfem/_par/tetrahedron.i b/mfem/_par/tetrahedron.i index 5cf34c91..7ca08dbf 100644 --- a/mfem/_par/tetrahedron.i +++ b/mfem/_par/tetrahedron.i @@ -1,8 +1,9 @@ %module(package="mfem._par") tetrahedron %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/tmop.i b/mfem/_par/tmop.i index 29333168..a657c705 100644 --- a/mfem/_par/tmop.i +++ b/mfem/_par/tmop.i @@ -2,8 +2,11 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pynonlininteg.hpp" %} %init %{ @@ -27,7 +30,7 @@ LIST_TO_MFEMOBJ_BOOLARRAY_IN(const mfem::Array& ) %import "../common/array_instantiation_macro.i" IGNORE_ARRAY_METHODS(mfem::TMOP_Integrator *) -INSTANTIATE_ARRAY0(TMOP_Integrator *, TMOP_Integrator, 1) +INSTANTIATE_ARRAY0(TMOP_Integrator *, TMOP_Integrator, 1) /* destructor handles freeing evaluator */ %pythonappend mfem::DiscreteAdaptTC::SetAdaptivityEvaluator %{ diff --git a/mfem/_par/tmop_amr.i b/mfem/_par/tmop_amr.i index 4ca0ea43..6cfb05a8 100644 --- a/mfem/_par/tmop_amr.i +++ b/mfem/_par/tmop_amr.i @@ -2,8 +2,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/tmop_tools.i b/mfem/_par/tmop_tools.i index b34de54a..b07d76d3 100644 --- a/mfem/_par/tmop_tools.i +++ b/mfem/_par/tmop_tools.i @@ -2,9 +2,10 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" -#include "../common/pysolvers.hpp" +#include "../common/pysolvers.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/transfer.i b/mfem/_par/transfer.i index 8bf3551b..969950d1 100644 --- a/mfem/_par/transfer.i +++ b/mfem/_par/transfer.i @@ -4,11 +4,11 @@ %{ #include "mfem.hpp" -#include "mesh/vertex.hpp" #include "numpy/arrayobject.h" -#include "fem/transfer.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ @@ -21,5 +21,5 @@ import_array(); %import "pfespace.i" %include "../common/exception.i" -%import "pyoperator.hpp" +%import "../common/pyoperator.hpp" %include "fem/transfer.hpp" diff --git a/mfem/_par/transfermap.i b/mfem/_par/transfermap.i index 9ede02c2..abec9bdf 100644 --- a/mfem/_par/transfermap.i +++ b/mfem/_par/transfermap.i @@ -5,8 +5,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_par/triangle.i b/mfem/_par/triangle.i index 05e8f074..76d548c7 100644 --- a/mfem/_par/triangle.i +++ b/mfem/_par/triangle.i @@ -1,8 +1,9 @@ %module(package="mfem._par") triangle %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/vector.i b/mfem/_par/vector.i index 45e8c931..62808ccf 100644 --- a/mfem/_par/vector.i +++ b/mfem/_par/vector.i @@ -12,9 +12,9 @@ #include #include #include -#include "mfem.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" %} // initialization required to return numpy array from SWIG @@ -43,15 +43,15 @@ ARRAY_TO_DOUBLEARRAY_IN(double *data_) %pythonprepend mfem::Vector::Vector %{ from numpy import ndarray, ascontiguousarray keep_link = False -own_data = False +own_data = False if len(args) == 1: - if isinstance(args[0], list): + if isinstance(args[0], list): args = (args[0], len(args[0])) - own_data = True + own_data = True elif isinstance(args[0], ndarray): if args[0].dtype != 'float64': raise ValueError('Must be float64 array ' + str(args[0].dtype) + - ' is given') + ' is given') else: args = (ascontiguousarray(args[0]), args[0].shape[0]) # in this case, args[0] need to be maintained @@ -70,28 +70,28 @@ if own_data: def __iadd__(self, v): ret = _vector.Vector___iadd__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self %} %feature("shadow") mfem::Vector::operator-= %{ def __isub__(self, v): ret = _vector.Vector___isub__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self -%} +%} %feature("shadow") mfem::Vector::operator*= %{ def __imul__(self, v): ret = _vector.Vector___imul__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self -%} +%} %feature("shadow") mfem::Vector::operator/= %{ def __itruediv__(self, v): ret = _vector.Vector___itruediv__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self %} //rename(Assign) mfem::Vector::operator=; @@ -104,15 +104,15 @@ if len(args) == 1: raise ValueError('Must be float64 array ' + str(args[0].dtype) + ' is given') elif args[0].ndim != 1: - raise ValueError('Ndim must be one') + raise ValueError('Ndim must be one') elif args[0].shape[0] != self.Size(): raise ValueError('Length does not match') else: args = (ascontiguousarray(args[0]),) elif isinstance(args[0], tuple): - args = (array(args[0], dtype = float),) - elif isinstance(args[0], list): - args = (array(args[0], dtype = float),) + args = (array(args[0], dtype = float),) + elif isinstance(args[0], list): + args = (array(args[0], dtype = float),) else: pass %} @@ -171,7 +171,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) /* define Assine as a replacement of = operator */ Vector(const mfem::Vector &v, int offset, int size){ mfem::Vector *vec; - vec = new mfem::Vector(v.GetData() + offset, size); + vec = new mfem::Vector(v.GetData() + offset, size); return vec; } void Assign(const double v) { @@ -198,25 +198,25 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) PyErr_SetString(PyExc_ValueError, "Input data NDIM must be one"); return ; } - npy_intp *shape = PyArray_DIMS(param0); + npy_intp *shape = PyArray_DIMS(param0); int len = self->Size(); - if (shape[0] != len){ + if (shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; - } + } (* self) = (double *) PyArray_DATA(param0); } void __setitem__(int i, const double v) { - int len = self->Size(); - if (i >= 0){ + int len = self->Size(); + if (i >= 0){ (* self)(i) = v; } else { (* self)(len+i) = v; } } PyObject* __getitem__(PyObject* param) { - int len = self->Size(); + int len = self->Size(); if (PySlice_Check(param)) { long start = 0, stop = 0, step = 0, slicelength = 0; int check; @@ -231,12 +231,12 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) if (check == -1) { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Vector failed."); - return NULL; + return NULL; } if (step == 1) { mfem::Vector *vec; vec = new mfem::Vector(self->GetData() + start, slicelength); - return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Vector *), 1); + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Vector *), 1); } else { mfem::Vector *vec; vec = new mfem::Vector(slicelength); @@ -254,7 +254,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) long idx = PyInt_AsLong(param); if (PyErr_Occurred()) { PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); - return NULL; + return NULL; } if ((idx >= len) && (idx >= -len-1)){ PyErr_SetString(PyExc_IndexError, "Index must be < Size (counting forward) or > -Size-1 (counting backward)"); @@ -268,7 +268,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) } } PyObject* GetDataArray(void) const{ - double * A = self->GetData(); + double * A = self->GetData(); int L = self->Size(); npy_intp dims[] = {L}; return PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, A); @@ -278,12 +278,12 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) if (!module){ PyErr_SetString(PyExc_RuntimeError, "Can not load io module"); return (PyObject *) NULL; - } + } PyObject* cls = PyObject_GetAttrString(module, "StringIO"); if (!cls){ PyErr_SetString(PyExc_RuntimeError, "Can not load StringIO"); return (PyObject *) NULL; - } + } int check = PyObject_IsInstance(StringIO, cls); Py_DECREF(module); if (! check){ @@ -291,7 +291,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) return (PyObject *) NULL; } std::ostringstream stream; - self->Print(stream, width); + self->Print(stream, width); std::string str = stream.str(); const char* s = str.c_str(); const int n = str.length(); diff --git a/mfem/_par/vertex.i b/mfem/_par/vertex.i index ad4388a1..3906e1cc 100644 --- a/mfem/_par/vertex.i +++ b/mfem/_par/vertex.i @@ -1,9 +1,10 @@ %module(package="mfem._par") vertex - + %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_par/vtk.i b/mfem/_par/vtk.i index a3398a27..a7a190af 100644 --- a/mfem/_par/vtk.i +++ b/mfem/_par/vtk.i @@ -1,9 +1,10 @@ %module(package="mfem._par") vtk %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %begin %{ #define PY_SSIZE_T_CLEAN diff --git a/mfem/_par/wedge.i b/mfem/_par/wedge.i index 935e82c3..f2248f32 100644 --- a/mfem/_par/wedge.i +++ b/mfem/_par/wedge.i @@ -2,8 +2,9 @@ %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/array.i b/mfem/_ser/array.i index 589b2e65..b65278c9 100644 --- a/mfem/_ser/array.i +++ b/mfem/_ser/array.i @@ -3,12 +3,12 @@ //%rename(Equal) mfem::Array ::operator=; %{ -#include +#include #include #include #include "../common/io_stream.hpp" #include "mfem.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %begin %{ @@ -43,7 +43,7 @@ XXXPTR_SIZE_IN(bool *data_, int asize, bool) %pythonappend mfem::Array::Array %{ if len(args) == 1 and isinstance(args[0], list): if (len(args[0]) == 2 and hasattr(args[0][0], 'disown') and - not hasattr(args[0][1], 'disown')): + not hasattr(args[0][1], 'disown')): ## first element is SwigObject, like ## We do not own data in this case. pass @@ -77,8 +77,8 @@ XXXPTR_SIZE_IN(bool *data_, int asize, bool) if (i >= 0){ (* self)[i] = v; } else { - int len = self->Size(); - (* self)[len+i] = v; + int len = self->Size(); + (* self)[len+i] = v; } } void Assign(const T &a){ @@ -143,12 +143,45 @@ OSTREAM_ADD_DEFAULT_STDOUT_FILE(Array2D, Save) #endif namespace mfem{ -%template(doubleSwap) Swap; -%template(intSwap) Swap; +%template(doubleSwap) Swap; +%template(intSwap) Swap; } +/* + Instantiation of Array templates. + + We instantiate some common use cases. Array.cpp instantiate these specialization. + + template class Array; + template class Array; + template class Array; + template class Array; + template class Array2D; + template class Array2D; +*/ + %import "../common/array_instantiation_macro.i" INSTANTIATE_ARRAY_INT INSTANTIATE_ARRAY_DOUBLE -IGNORE_ARRAY_METHODS(bool) +INSTANTIATE_ARRAY_NUMPYARRAY(int8, char, NPY_BYTE) // for 8bit data +INSTANTIATE_ARRAY_NUMPYARRAY(int64, long long, NPY_LONGLONG) // 64bit + + /* +For other classes, we need to ignore some methods + To ignore methos defined in Array.cpp, we use + IGNORE_ARRAY_METHODS_PREMITIVE + In more genral object, we need to futher ignore methods which uses comparision (> or == operators). + IGNORE_ARRAY_METHODS + */ + +IGNORE_ARRAY_METHODS_PREMITIVE(bool) INSTANTIATE_ARRAY_BOOL +IGNORE_ARRAY_METHODS_PREMITIVE(unsigned int) +INSTANTIATE_ARRAY_NUMPYARRAY(uint, unsigned int, NPY_UINT) // 32bit + +/* + for these Array2D, we instantiate it. But we dont extend it since, Array2D does not + expose the interanl pointer to array1d. +*/ +%template(intArray2D) mfem::Array2D; +%template(doubleArray2D) mfem::Array2D; diff --git a/mfem/_ser/bilinearform.i b/mfem/_ser/bilinearform.i index e8b8840e..c2876bc9 100644 --- a/mfem/_ser/bilinearform.i +++ b/mfem/_ser/bilinearform.i @@ -2,9 +2,11 @@ %{ #include "fem/bilinearform.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -using namespace mfem; +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +using namespace mfem; %} %init %{ @@ -27,12 +29,14 @@ import_array(); %import "bilininteg.i" %import "linearform.i" %import "gridfunc.i" +%import "hybridization.i" +%import "staticcond.i" %include "../common/exception_director.i" -%feature("director") mfem::BilinearForm; +//%feature("director") mfem::BilinearForm; //%include "fem/coefficient.hpp" -namespace mfem { +namespace mfem { %pythonprepend BilinearForm::AddDomainIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] bfi = args[0] @@ -45,15 +49,15 @@ namespace mfem { bfi = args[0] self._integrators.append(bfi) self.UseExternalIntegrators() - #bfi.thisown=0 - %} + #bfi.thisown=0 + %} %pythonprepend BilinearForm::AddBdrFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] bfi = args[0] self._integrators.append(bfi) self.UseExternalIntegrators() #bfi.thisown=0 - %} + %} %pythonprepend BilinearForm::AddInteriorFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(bfi) @@ -70,9 +74,10 @@ namespace mfem { self._integrators.append(constr_integ) # constr_integ is deleted by Hybridization destructor constr_integ.thisown = 0 - %} + %} %pythonprepend MixedBilinearForm::AddDomainIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] + bfi = args[0] self._integrators.append(bfi) bfi.thisown=0 %} @@ -81,7 +86,7 @@ namespace mfem { bfi = args[0] self._integrators.append(bfi) bfi.thisown=0 - %} + %} %pythonprepend MixedBilinearForm::AddTraceFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(bfi) @@ -92,8 +97,8 @@ namespace mfem { bfi = args[0] self._integrators.append(bfi) self.UseExternalIntegrators() - #bfi.thisown=0 - %} + #bfi.thisown=0 + %} %pythonappend MixedBilinearForm::SpMat %{ if not hasattr(self, "_spmat"): self._spmat = [] self._spmat.append(val) @@ -101,11 +106,13 @@ namespace mfem { %} %pythonprepend DiscreteLinearOperator::AddDomainInterpolator %{ if not hasattr(self, "_integrators"): self._integrators = [] + di = args[0] self._integrators.append(di) di.thisown=0 - %} + %} %pythonprepend DiscreteLinearOperator::AddTraceFaceInterpolator %{ if not hasattr(self, "_integrators"): self._integrators = [] + di = args[0] self._integrators.append(di) di.thisown=0 %} @@ -128,10 +135,12 @@ INSTANTIATE_ARRAY0(BilinearForm *, BilinearForm, 1) %include "fem/bilinearform.hpp" -// instatitate template methods +// instatitate template methods %define FORM_SYSTEM_MATRIX_WRAP(OsType) %template(FormLinearSystem) mfem::BilinearForm::FormLinearSystem; %template(FormSystemMatrix) mfem::BilinearForm::FormSystemMatrix; +%template(FormRectangularLinearSystem) mfem::MixedBilinearForm::FormRectangularLinearSystem; +%template(FormRectangularSystemMatrix) mfem::MixedBilinearForm::FormRectangularSystemMatrix; %enddef FORM_SYSTEM_MATRIX_WRAP(SparseMatrix) @@ -141,7 +150,7 @@ FORM_SYSTEM_MATRIX_WRAP(SparseMatrix) FORM_SYSTEM_MATRIX_WRAP(mfem::HypreParMatrix) #endif */ - + #ifdef MFEM_USE_PETSC FORM_SYSTEM_MATRIX_WRAP(mfem::PetscParMatrix) -#endif +#endif diff --git a/mfem/_ser/bilininteg.i b/mfem/_ser/bilininteg.i index 98b09790..1acb4445 100644 --- a/mfem/_ser/bilininteg.i +++ b/mfem/_ser/bilininteg.i @@ -1,8 +1,11 @@ %module(package="mfem._ser", directors="1") bilininteg %{ #include "mfem.hpp" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pynonlininteg.hpp" #include "numpy/arrayobject.h" //using namespace mfem; %} @@ -11,17 +14,6 @@ import_array(); %} -/* -%exception { - try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } - //catch (...){ - // SWIG_fail; - //} - // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } -} -*/ %include "exception.i" %import "globals.i" @@ -41,17 +33,12 @@ import_array(); %import "fe.i" %import "nonlininteg.i" %include "../common/exception_director.i" - //%template(IntegrationPointArray) mfem::Array; - - //%feature("director:except") { - // if ($error != NULL) { - // throw Swig::DirectorMethodException(); - // } - //} -%feature("director") mfem::BilinearFormIntegrator; %include "../common/bilininteg_ext.i" %ignore mfem::MassIntegrator::SetupPA; %include "fem/bilininteg.hpp" + +%feature("director") mfem::PyBilinearFormIntegrator; +%include "../common/pybilininteg.hpp" diff --git a/mfem/_ser/blockmatrix.i b/mfem/_ser/blockmatrix.i index ae02fc92..6f294875 100644 --- a/mfem/_ser/blockmatrix.i +++ b/mfem/_ser/blockmatrix.i @@ -1,12 +1,12 @@ %module(package="mfem._ser") blockmatrix %{ -#include +#include #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/io_stream.hpp" %} // initialization required to return numpy array from SWIG %init %{ @@ -26,7 +26,7 @@ import_array(); OSTREAM_TYPEMAP(std::ostream&) %pythonappend mfem::BlockMatrix::BlockMatrix %{ -from mfem.ser import intArray +from mfem.ser import intArray if len(args) == 1: if isinstance(args[0], intArray): self._offsets = args[0] diff --git a/mfem/_ser/blockoperator.i b/mfem/_ser/blockoperator.i index 3a05b613..53ba7c1f 100644 --- a/mfem/_ser/blockoperator.i +++ b/mfem/_ser/blockoperator.i @@ -3,9 +3,9 @@ %{ #include "linalg/blockoperator.hpp" #include "linalg/operator.hpp" -#include "linalg/sparsemat.hpp" +#include "linalg/sparsemat.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} // initialization required to return numpy array from SWIG %init %{ @@ -18,7 +18,7 @@ import_array(); %import "../common/exception.i" %pythonappend mfem::BlockOperator::BlockOperator %{ -from mfem.ser import intArray +from mfem.ser import intArray if len(args) == 1: if isinstance(args[0], intArray): self._offsets = args[0] @@ -31,7 +31,7 @@ if len(args) == 2: if not hasattr(self, '_linked_op'): self._linked_op = {} self._linked_op[iblock, iblock] = op -%} +%} %pythonappend mfem::BlockOperator::SetBlock %{ if not hasattr(self, '_linked_op'): self._linked_op = {} @@ -65,7 +65,7 @@ if len(args) == 2: self._linked_op = {} self._linked_op[iRow, iCol] = op -%} +%} %inline %{ mfem::BlockOperator *Opr2BlockOpr(mfem::Operator *op) { diff --git a/mfem/_ser/coefficient.i b/mfem/_ser/coefficient.i index 8bd6736c..7c37066d 100644 --- a/mfem/_ser/coefficient.i +++ b/mfem/_ser/coefficient.i @@ -20,10 +20,12 @@ #include #include #include -#include "mfem.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} // initialization required to return numpy array from SWIG @@ -57,10 +59,10 @@ namespace mfem { if can_np_array: v = mfem._ser.vector.Vector(np.transpose(value).flatten()) - m = mfem._ser.densemat.DenseMatrix(v.GetData(), value.shape[0], value.shape[1]) + m = mfem._ser.densemat.DenseMatrix(v.GetData(), value.shape[0], value.shape[1]) self._value = (v,m) else: - pass + pass %} %pythonprepend VectorConstantCoefficient::VectorConstantCoefficient(const Vector &v) %{ try: @@ -74,7 +76,7 @@ namespace mfem { v = mfem._ser.vector.Vector(value) self._value = v else: - pass + pass %} } %include "../common/coefficient_common.i" @@ -93,12 +95,12 @@ namespace mfem { /* %exception { try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } + catch (Swig::DirectorException &e) { SWIG_fail; } //catch (...){ // SWIG_fail; //} // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } + // catch (std::exception &e) { SWIG_fail; } } %feature("director:except") { if ($error != NULL) { @@ -141,7 +143,7 @@ void fake_func_mat(const mfem::Vector &x, mfem::DenseMatrix &Kt) Kt(1,2) = 0.0; Kt(2,2) = 1.0; } -namespace mfem{ +namespace mfem{ double PyCoefficientBase::Eval(ElementTransformation &T, const IntegrationPoint &ip) { @@ -170,7 +172,7 @@ void VectorPyCoefficientBase::Eval(Vector &V, ElementTransformation &T, V.SetSize(vdim); if (isTimeDependent) { - _EvalPyT(transip, GetTime(), V); + _EvalPyT(transip, GetTime(), V); } else { @@ -200,10 +202,10 @@ void MatrixPyCoefficientBase::Eval(DenseMatrix &K, ElementTransformation &T, Vector transip(x, 3); T.Transform(ip, transip); - K.SetSize(height, width); + K.SetSize(height, width); if (isTimeDependent) { - _EvalPyT(transip, GetTime(), K); + _EvalPyT(transip, GetTime(), K); } else { @@ -223,7 +225,7 @@ class PyCoefficient(PyCoefficientBase): return self.EvalValue(x.GetDataArray()) def EvalValue(self, x): return 0.0 - + class PyCoefficientT(PyCoefficientBase): def __init__(self): PyCoefficientBase.__init__(self, 1) @@ -231,7 +233,7 @@ class PyCoefficientT(PyCoefficientBase): return self.EvalValue(x.GetDataArray(), t) def EvalValue(self, x, t): return 0.0 - + class VectorPyCoefficient(VectorPyCoefficientBase): def __init__(self, dim): self.vdim = dim @@ -242,22 +244,22 @@ class VectorPyCoefficient(VectorPyCoefficientBase): def _EvalPyT(self, x, t, V): v = self.EvalValue(x.GetDataArray()) - V.Assign(v) + V.Assign(v) def EvalValue(self, x): return [0,0,0] - + class VectorPyCoefficientT(VectorPyCoefficientBase): def __init__(self, dim): - self.vdim = dim + self.vdim = dim VectorPyCoefficientBase.__init__(self, dim, 1) def _EvalPy(self, x, V): v = self.EvalValue(x.GetDataArray(), 0) - V.Assign(v) + V.Assign(v) def _EvalPyT(self, x, t, V): v = self.EvalValue(x.GetDataArray(), t) - V.Assign(v) + V.Assign(v) def EvalValue(self, x, t): return [0,0,0] @@ -268,21 +270,21 @@ class MatrixPyCoefficient(MatrixPyCoefficientBase): MatrixPyCoefficientBase.__init__(self, dim, 0) def _EvalPy(self, x, K): k = self.EvalValue(x.GetDataArray()) - K.Assign(k) + K.Assign(k) def EvalValue(self, x): return np.array([[0,0,0], [0,0,0], [0,0,0]]) - + class MatrixPyCoefficientT(MatrixPyCoefficientBase): def __init__(self, dim): - self.vdim = dim + self.vdim = dim MatrixPyCoefficientBase.__init__(self, dim, 1) def _EvalPyT(self, x, t, K): k = self.EvalValue(x.GetDataArray(), t) - K.Assign(k) + K.Assign(k) def EvalValue(self, x, t): return np.array([[0,0,0], [0,0,0], [0,0,0]]) - + %} diff --git a/mfem/_ser/common_functions.i b/mfem/_ser/common_functions.i index 396f743a..978d5dac 100644 --- a/mfem/_ser/common_functions.i +++ b/mfem/_ser/common_functions.i @@ -4,9 +4,9 @@ #include #include #include "mfem.hpp" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} %init %{ import_array(); diff --git a/mfem/_ser/complex_fem.i b/mfem/_ser/complex_fem.i index 1572b486..97e7596f 100644 --- a/mfem/_ser/complex_fem.i +++ b/mfem/_ser/complex_fem.i @@ -6,11 +6,14 @@ %module(package="mfem._ser") complex_fem %feature("autodoc", "1"); %{ -#include "fem/complex_fem.hpp" +#include "fem/complex_fem.hpp" #include "linalg/complex_operator.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pylininteg.hpp" %} %init %{ import_array(); diff --git a/mfem/_ser/complex_operator.i b/mfem/_ser/complex_operator.i index 84c7f0f2..9f60b0d4 100644 --- a/mfem/_ser/complex_operator.i +++ b/mfem/_ser/complex_operator.i @@ -8,7 +8,7 @@ %{ #include "linalg/complex_operator.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" %} %init %{ import_array(); @@ -19,14 +19,14 @@ import_array(); %import "operators.i" %import "sparsemat.i" -namespace mfem { +namespace mfem { %pythonprepend ComplexOperator::ComplexOperator %{ self._parts = [Op_Real, Op_Imag] if ownReal: assert Op_Real.thisown != 0, "Real Op is not owned by passed object" Op_Real.thisown = 0 if ownImag: - assert Op_Real.thisown != 0, "Imag Op is not owned by passed object" + assert Op_Real.thisown != 0, "Imag Op is not owned by passed object" Op_Imag.thisown = 0 %} %ignore ComplexOperator::ComplexOperator(Operator * Op_Real, Operator * Op_Imag, diff --git a/mfem/_ser/constraints.i b/mfem/_ser/constraints.i index 3c681feb..db263464 100644 --- a/mfem/_ser/constraints.i +++ b/mfem/_ser/constraints.i @@ -6,15 +6,12 @@ %module(package="mfem._ser") constraints %feature("autodoc", "1"); %{ -#include "linalg/constraints.hpp" -#include "fem/restriction.hpp" -#include "fem/linearform.hpp" -#include "linalg/complex_operator.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" #include "../common/pysolvers.hpp" - +#include "../common/pyintrules.hpp" %} %init %{ import_array(); diff --git a/mfem/_ser/datacollection.i b/mfem/_ser/datacollection.i index c6574763..8033ea59 100644 --- a/mfem/_ser/datacollection.i +++ b/mfem/_ser/datacollection.i @@ -1,9 +1,10 @@ %module(package="mfem._ser") datacollection %{ #include "mfem.hpp" -#include "pyoperator.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/densemat.i b/mfem/_ser/densemat.i index a9db5e3f..721ea204 100644 --- a/mfem/_ser/densemat.i +++ b/mfem/_ser/densemat.i @@ -11,9 +11,9 @@ #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/io_stream.hpp" -using namespace mfem; +using namespace mfem; %} // initialization required to return numpy array from SWIG %init %{ @@ -55,7 +55,7 @@ if len(args) == 1 and isinstance(args[0], ndarray): if args[0].dtype != 'float64': raise ValueError('Must be float64 array:' + str(args[0].dtype) + ' was given') elif args[0].ndim != 2: - raise ValueError('Ndim must be two') + raise ValueError('Ndim must be two') elif args[0].shape[1] != _densemat.DenseMatrix_Size(self): raise ValueError('Length does not match') else: @@ -72,23 +72,23 @@ if len(args) == 1 and isinstance(args[0], ndarray): def __iadd__(self, v): ret = _densemat.DenseMatrix___iadd__(self, v) ret.thisown = self.thisown - self.thisown = 0 + self.thisown = 0 return ret %} %feature("shadow") mfem::DenseMatrix::operator-= %{ def __isub__(self, v): - ret = _densemat.DenseMatrix___isub__(self, v) + ret = _densemat.DenseMatrix___isub__(self, v) ret.thisown = self.thisown - self.thisown = 0 + self.thisown = 0 return ret -%} +%} %feature("shadow") mfem::DenseMatrix::operator*= %{ def __imul__(self, v): - ret = _densemat.DenseMatrix___imul__(self, v) + ret = _densemat.DenseMatrix___imul__(self, v) ret.thisown = self.thisown - self.thisown = 0 + self.thisown = 0 return ret -%} +%} %feature("shadow") mfem::DenseMatrix::__setitem__%{ def __setitem__(self, *args): i, j, v = args[0][0], args[0][1], args[1] @@ -98,7 +98,7 @@ def __setitem__(self, *args): def __getitem__(self, *args): i, j = args[0][0], args[0][1] return _densemat.DenseMatrix___getitem__(self, i, j) -%} +%} %feature("shadow") mfem::DenseTensor::__setitem__%{ def __setitem__(self, *args): i, j, k, v = args[0][0], args[0][1], args[0][2], args[1] @@ -117,9 +117,9 @@ def __getitem__(self, *args): check = int(args[0]) except: check = -1 - if check >= 0: + if check >= 0: return _densemat.DenseTensor___getitem__(self, check) -%} +%} %include "linalg/densemat.hpp" @@ -142,7 +142,7 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data NDIM must be 2"); return NULL; } - npy_intp *shape = PyArray_DIMS(numpymat0); + npy_intp *shape = PyArray_DIMS(numpymat0); return new mfem::DenseMatrix(shape[0], shape[1]); } @@ -171,21 +171,21 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data NDIM must be 2"); return ; } - npy_intp *shape = PyArray_DIMS(numpymat0); + npy_intp *shape = PyArray_DIMS(numpymat0); int len = self->Width()*self->Height(); - if (shape[1]*shape[0] != len){ + if (shape[1]*shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; } - PyObject * tmp1 = + PyObject * tmp1 = PyArray_Transpose(numpymat0, NULL); - PyArrayObject * tmp2 = + PyArrayObject * tmp2 = PyArray_GETCONTIGUOUS((PyArrayObject *)tmp1); (* self) = (double *) PyArray_DATA(tmp2); Py_XDECREF(tmp1); - Py_XDECREF(tmp2); + Py_XDECREF(tmp2); } - + const double __getitem__(const int i, const int j) const{ return (* self)(i, j); } @@ -193,13 +193,13 @@ def __getitem__(self, *args): (* self)(i, j) = v; } PyObject* GetDataArray(void) const{ - double * A = self->Data(); + double * A = self->Data(); npy_intp dims[] = {self->Width(), self->Height()}; PyObject *tmp1 = PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, A); PyObject *ret = PyArray_Transpose((PyArrayObject *)tmp1, NULL); Py_XDECREF(tmp1); return ret; - + //return PyArray_Transpose((PyArrayObject *)PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, A), NULL); } }; @@ -218,7 +218,7 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data must be ndarray"); return; } - PyArrayObject *numpymat0 = reinterpret_cast(numpymat); + PyArrayObject *numpymat0 = reinterpret_cast(numpymat); int typ = PyArray_TYPE(numpymat0); if (typ != NPY_DOUBLE){ PyErr_SetString(PyExc_ValueError, "Input data must be float64"); @@ -229,22 +229,22 @@ def __getitem__(self, *args): PyErr_SetString(PyExc_ValueError, "Input data NDIM must be 3"); return ; } - npy_intp *shape = PyArray_DIMS(numpymat0); + npy_intp *shape = PyArray_DIMS(numpymat0); int len = self->SizeI()*self->SizeJ()*self->SizeK(); - if (shape[2]*shape[1]*shape[0] != len){ + if (shape[2]*shape[1]*shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; } for (int i=0; i < self->SizeI(); i++){ for (int j=0; j < self->SizeJ(); j++){ - for (int k=0; k < self->SizeK(); k++){ + for (int k=0; k < self->SizeK(); k++){ (* self)(i, j, k) = *(double *) PyArray_GETPTR3(numpymat0, i, j, k); } } } } - + const double __getitem__(const int i, const int j, const int k) const{ return (* self)(i, j, k); } @@ -256,12 +256,12 @@ def __getitem__(self, *args): } PyObject* GetDataArray(void){ // DoDo this method can not be const since DenseTensor::Data is not const - double * A = self->Data(); + double * A = self->Data(); npy_intp dims[] = {self->SizeK(), self->SizeJ(), self->SizeI()}; PyObject * obj = PyArray_SimpleNewFromData(3, dims, NPY_DOUBLE, A); //obj = PyArray_SwapAxes((PyArrayObject *)obj, 0, 2); PyObject * ret = PyArray_SwapAxes((PyArrayObject *)obj, 1, 2); - Py_XDECREF(obj); + Py_XDECREF(obj); return ret; } }; @@ -274,5 +274,5 @@ def __getitem__(self, *args): #ifndef SWIGIMPORTED OSTREAM_ADD_DEFAULT_FILE(DenseMatrix, Print) OSTREAM_ADD_DEFAULT_FILE(DenseMatrix, PrintT) -OSTREAM_ADD_DEFAULT_FILE(DenseMatrix, PrintMatlab) +OSTREAM_ADD_DEFAULT_FILE(DenseMatrix, PrintMatlab) #endif diff --git a/mfem/_ser/device.i b/mfem/_ser/device.i index 3f596e73..33f78c91 100644 --- a/mfem/_ser/device.i +++ b/mfem/_ser/device.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/device.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ @@ -27,7 +27,7 @@ DEPRECATED_METHOD(mfem::Device::GetMemoryClass()) %} %feature("shadow") mfem::Device::__new__ %{ def __new__(cls, *args, **kwargs): - if globals()["singleton_device"] is None: + if globals()["singleton_device"] is None: instance = super(Device, cls).__new__(cls) globals()["singleton_device"] = instance return globals()["singleton_device"] diff --git a/mfem/_ser/doftrans.i b/mfem/_ser/doftrans.i index 7d707bfa..485f6726 100644 --- a/mfem/_ser/doftrans.i +++ b/mfem/_ser/doftrans.i @@ -1,15 +1,17 @@ %module(package="mfem._ser") doftrans %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ import_array(); %} %include "exception.i" -%import "fe.i" +%import "vector.i" +%import "densemat.i" %import "intrules.i" %include "../common/typemap_macros.i" %include "../common/exception.i" diff --git a/mfem/_ser/element.i b/mfem/_ser/element.i index a11c2989..19c517b9 100644 --- a/mfem/_ser/element.i +++ b/mfem/_ser/element.i @@ -1,10 +1,11 @@ %module(package="mfem._ser") element %{ -#include +#include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/eltrans.i b/mfem/_ser/eltrans.i index 7bb3772a..caeaf574 100644 --- a/mfem/_ser/eltrans.i +++ b/mfem/_ser/eltrans.i @@ -2,9 +2,10 @@ %{ #include "mfem.hpp" -#include "pyoperator.hpp" #include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" #include "../common/io_stream.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/error.i b/mfem/_ser/error.i index 69a20023..ff150910 100644 --- a/mfem/_ser/error.i +++ b/mfem/_ser/error.i @@ -1,9 +1,9 @@ %module(package="mfem._ser") error %{ -#include +#include #include #include -#include "general/error.hpp" +#include "general/error.hpp" %} %include "exception.i" %include "../common/exception.i" diff --git a/mfem/_ser/estimators.i b/mfem/_ser/estimators.i index 041ba379..77136c9e 100644 --- a/mfem/_ser/estimators.i +++ b/mfem/_ser/estimators.i @@ -3,8 +3,10 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} // initialization required to return numpy array from SWIG %init %{ diff --git a/mfem/_ser/fe.i b/mfem/_ser/fe.i index 66bbe771..6b933a85 100644 --- a/mfem/_ser/fe.i +++ b/mfem/_ser/fe.i @@ -1,10 +1,11 @@ %module(package="mfem._ser") fe %{ -#include +#include #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_base.i b/mfem/_ser/fe_base.i index 698c9d14..aa26bc87 100644 --- a/mfem/_ser/fe_base.i +++ b/mfem/_ser/fe_base.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_base %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -11,6 +12,7 @@ import_array(); %include "exception.i" %import "intrules.i" %import "geom.i" +%import "doftrans.i" %include "../common/typemap_macros.i" %include "../common/exception.i" diff --git a/mfem/_ser/fe_coll.i b/mfem/_ser/fe_coll.i index 02759f52..6d379fcc 100644 --- a/mfem/_ser/fe_coll.i +++ b/mfem/_ser/fe_coll.i @@ -7,10 +7,11 @@ #include #include #include -#include "mfem.hpp" -#include "pyoperator.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -38,5 +39,5 @@ import_array(); %include "fem/fe_coll.hpp" %pythoncode %{ DG_FECollection = L2_FECollection -%} +%} diff --git a/mfem/_ser/fe_fixed_order.i b/mfem/_ser/fe_fixed_order.i index 06de5a4c..c469efc3 100644 --- a/mfem/_ser/fe_fixed_order.i +++ b/mfem/_ser/fe_fixed_order.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_fixed_order %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_h1.i b/mfem/_ser/fe_h1.i index bb0f5697..eee8acf8 100644 --- a/mfem/_ser/fe_h1.i +++ b/mfem/_ser/fe_h1.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_h1 %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_l2.i b/mfem/_ser/fe_l2.i index 0630f6af..91da2b74 100644 --- a/mfem/_ser/fe_l2.i +++ b/mfem/_ser/fe_l2.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_l2 %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_nd.i b/mfem/_ser/fe_nd.i index b8aa01ac..80d9bbd2 100644 --- a/mfem/_ser/fe_nd.i +++ b/mfem/_ser/fe_nd.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_nd %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_nurbs.i b/mfem/_ser/fe_nurbs.i index 4c07ac4d..81f6b2b1 100644 --- a/mfem/_ser/fe_nurbs.i +++ b/mfem/_ser/fe_nurbs.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_nurbs %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_pos.i b/mfem/_ser/fe_pos.i index b4a0fcb4..af957809 100644 --- a/mfem/_ser/fe_pos.i +++ b/mfem/_ser/fe_pos.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_pos %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_rt.i b/mfem/_ser/fe_rt.i index 8a95ad17..0bcd8be4 100644 --- a/mfem/_ser/fe_rt.i +++ b/mfem/_ser/fe_rt.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_rt %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fe_ser.i b/mfem/_ser/fe_ser.i index 203951b8..90fe8869 100644 --- a/mfem/_ser/fe_ser.i +++ b/mfem/_ser/fe_ser.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") fe_ser %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/fespace.i b/mfem/_ser/fespace.i index 5d4f7393..fd26643b 100644 --- a/mfem/_ser/fespace.i +++ b/mfem/_ser/fespace.i @@ -8,18 +8,12 @@ #include #include #include - -#include "../common/io_stream.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "fem/fem.hpp" -#include "fem/fe_coll.hpp" -#include "fem/fespace.hpp" -#include "fem/eltrans.hpp" -#include "fem/coefficient.hpp" -#include "fem/intrules.hpp" -#include "fem/restriction.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -170,7 +164,7 @@ def GetEdgeInteriorDofs(self, i): if hasattr(self, 'this'): self.mesh = args[0] self.fec = args[1] - + %} /* define FiniteElementSpacePtrArray */ @@ -204,12 +198,12 @@ OSTREAM_ADD_DEFAULT_STDOUT_FILE(QuadratureSpace, Save) return self->GetBdrElementDofs(bel, dofs); } virtual DofTransformation *GetElementVDofTransformation(int elem) const { - mfem::Array dofs; + mfem::Array dofs; return self->GetElementVDofs(elem, dofs); } virtual DofTransformation *GetBdrElementVDofTransformation(int bel) const { - mfem::Array dofs; + mfem::Array dofs; return self->GetBdrElementVDofs(bel, dofs); } }; - + diff --git a/mfem/_ser/fespacehierarchy.i b/mfem/_ser/fespacehierarchy.i index 45afcbeb..9ef32592 100644 --- a/mfem/_ser/fespacehierarchy.i +++ b/mfem/_ser/fespacehierarchy.i @@ -8,8 +8,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ import_array(); diff --git a/mfem/_ser/geom.i b/mfem/_ser/geom.i index a1ec05f5..0da39f1b 100644 --- a/mfem/_ser/geom.i +++ b/mfem/_ser/geom.i @@ -2,8 +2,10 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ @@ -45,7 +47,7 @@ namespace mfem{ return (* self)[i]; } }; - + %pythoncode %{ Geometries = Geometry() %} diff --git a/mfem/_ser/globals.i b/mfem/_ser/globals.i index e217f00b..526ca8d7 100644 --- a/mfem/_ser/globals.i +++ b/mfem/_ser/globals.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/globals.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_ser/gridfunc.i b/mfem/_ser/gridfunc.i index 33c1a765..266c30c3 100644 --- a/mfem/_ser/gridfunc.i +++ b/mfem/_ser/gridfunc.i @@ -2,26 +2,29 @@ %feature("autodoc", "1"); %begin %{ -#ifndef PY_SSIZE_T_CLEAN +#ifndef PY_SSIZE_T_CLEAN #define PY_SSIZE_T_CLEAN #endif %} %{ - #include + #include #include #include #include #include #include #include - #include "mfem/mfem.hpp" - #include "../common/pycoefficient.hpp" - #include "pyoperator.hpp" + #include "mfem/mfem.hpp" #include "numpy/arrayobject.h" #include "../common/io_stream.hpp" - using namespace mfem; + #include "../common/pycoefficient.hpp" + #include "../common/pyoperator.hpp" + #include "../common/pyintrules.hpp" + #include "../common/pybilininteg.hpp" + + using namespace mfem; %} // initialization required to return numpy array from SWIG %init %{ @@ -77,9 +80,9 @@ LIST_TO_MFEMOBJ_POINTERARRAY_IN(mfem::IntegrationRule const *irs[], mfem::Integ namespace mfem{ %extend GridFunction{ - + GridFunction(mfem::FiniteElementSpace *fes, const mfem::Vector &v, int offset){ - mfem::GridFunction *gf; + mfem::GridFunction *gf; gf = new mfem::GridFunction(fes, v.GetData() + offset); return gf; } @@ -91,12 +94,12 @@ GridFunction(mfem::FiniteElementSpace *fes, const mfem::Vector &v, int offset){ } void Assign(const mfem::GridFunction &v) { (* self) = v; - } + } void Assign(PyObject* param) { /* note that these error does not raise error in python type check is actually done in wrapper layer */ PyArrayObject *param0 = reinterpret_cast(param); - + if (!PyArray_Check(param0)){ PyErr_SetString(PyExc_ValueError, "Input data must be ndarray"); return; @@ -111,21 +114,21 @@ GridFunction(mfem::FiniteElementSpace *fes, const mfem::Vector &v, int offset){ PyErr_SetString(PyExc_ValueError, "Input data NDIM must be one"); return ; } - npy_intp *shape = PyArray_DIMS(param0); + npy_intp *shape = PyArray_DIMS(param0); int len = self->Size(); - if (shape[0] != len){ + if (shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; - } + } (Vector &)(* self) = (double *) PyArray_DATA(param0); } void SaveToFile(const char *gf_file, const int precision) const { std::cerr << "\nWarning Deprecated : Use Save(filename) insteead of SaveToFile \n"; - std::ofstream mesh_ofs(gf_file); + std::ofstream mesh_ofs(gf_file); mesh_ofs.precision(precision); - self->Save(mesh_ofs); + self->Save(mesh_ofs); } PyObject* WriteToStream(PyObject* StringIO) const { @@ -133,12 +136,12 @@ PyObject* WriteToStream(PyObject* StringIO) const { if (!module){ PyErr_SetString(PyExc_RuntimeError, "Can not load io module"); return (PyObject *) NULL; - } + } PyObject* cls = PyObject_GetAttrString(module, "StringIO"); if (!cls){ PyErr_SetString(PyExc_RuntimeError, "Can not load StringIO"); return (PyObject *) NULL; - } + } int check = PyObject_IsInstance(StringIO, cls); Py_DECREF(module); if (! check){ @@ -155,9 +158,9 @@ PyObject* WriteToStream(PyObject* StringIO) const { PyErr_SetString(PyExc_RuntimeError, "Error occured when writing IOString"); return (PyObject *) NULL; } - return ret; + return ret; } - +/* GridFunction & iadd(GridFunction &c) { *self += c; @@ -183,9 +186,10 @@ GridFunction & idiv(double c) * self /= c; return *self; } - } -} - +*/ + } // end of extend + } //end of namespace + /* %pythoncode %{ def __iadd__(self, v): ret = _gridfunc.GridFunction_iadd(self, v) @@ -207,8 +211,9 @@ def __imul__(self, v): GridFunction.__iadd__ = __iadd__ GridFunction.__idiv__ = __idiv__ GridFunction.__isub__ = __isub__ -GridFunction.__imul__ = __imul__ -%} +GridFunction.__imul__ = __imul__ +%} + */ /* fem/gridfunc.hpp: virtual void Save(std::ostream &out) const; @@ -219,5 +224,5 @@ fem/gridfunc.hpp: void SaveSTL(std::ostream &out, int TimesToRefine = 1); #ifndef SWIGIMPORTED OSTREAM_ADD_DEFAULT_FILE(GridFunction, Save) OSTREAM_ADD_DEFAULT_FILE(QuadratureFunction, Save) -#endif - +#endif + diff --git a/mfem/_ser/gslib.i b/mfem/_ser/gslib.i index e8c0366c..da079466 100644 --- a/mfem/_ser/gslib.i +++ b/mfem/_ser/gslib.i @@ -3,8 +3,9 @@ #include "mfem.hpp" #include "fem/gslib.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/mfem_config.i" @@ -16,6 +17,7 @@ import_array(); %include "exception.i" %include "../common/typemap_macros.i" %include "../common/exception.i" +%import array.i %import vector.i %import mesh.i %import gridfunc.i diff --git a/mfem/_ser/handle.i b/mfem/_ser/handle.i index 4aa323af..7471aea4 100644 --- a/mfem/_ser/handle.i +++ b/mfem/_ser/handle.i @@ -1,17 +1,17 @@ %module(package="mfem._ser") handle %feature("autodoc", "1"); %{ -#include +#include #include -#include "../common/io_stream.hpp" -#include "config/config.hpp" +#include "../common/io_stream.hpp" +#include "config/config.hpp" #include "linalg/hypre.hpp" -#include "linalg/handle.hpp" -#include "fem/gridfunc.hpp" +#include "linalg/handle.hpp" +#include "fem/gridfunc.hpp" #include "fem/linearform.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#ifdef MFEM_USE_MPI +#include "../common/pyoperator.hpp" +#ifdef MFEM_USE_MPI #include "fem/pfespace.hpp" #endif %} @@ -56,7 +56,7 @@ CONVERT_FROM_RENAME(SparseMatrix) %include "linalg/handle.hpp" %pythoncode %{ -OperatorPtr=OperatorHandle +OperatorPtr=OperatorHandle %} // instatitate template methods (step 2: Instantiation) @@ -64,7 +64,7 @@ OperatorPtr=OperatorHandle AS_WRAP(SparseMatrix) IS_WRAP(SparseMatrix) GET_WRAP(SparseMatrix) -RESET_WRAP(SparseMatrix) +RESET_WRAP(SparseMatrix) CONVERT_FROM_WRAP(SparseMatrix) diff --git a/mfem/_ser/hexahedron.i b/mfem/_ser/hexahedron.i index 5e3ae9a6..6c9118a9 100644 --- a/mfem/_ser/hexahedron.i +++ b/mfem/_ser/hexahedron.i @@ -1,9 +1,10 @@ %module(package="mfem._ser") hexahedron - + %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/hybridization.i b/mfem/_ser/hybridization.i index dd99b4fb..91f6dd87 100644 --- a/mfem/_ser/hybridization.i +++ b/mfem/_ser/hybridization.i @@ -1,9 +1,11 @@ %module(package="mfem._ser") hybridization %{ -#include "mfem.hpp" -#include "pyoperator.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ diff --git a/mfem/_ser/intrules.i b/mfem/_ser/intrules.i index 39522afc..c8fcc4be 100644 --- a/mfem/_ser/intrules.i +++ b/mfem/_ser/intrules.i @@ -3,6 +3,7 @@ %{ #include "fem/intrules.hpp" #include "numpy/arrayobject.h" +#include "../common/pyintrules.hpp" %} %init %{ @@ -15,7 +16,6 @@ import_array(); %import "../common/numpy_int_typemap.i" %import "mem_manager.i" - %immutable IntRules; %immutable RefinedIntRules; @@ -35,3 +35,7 @@ IGNORE_ARRAY_METHODS(mfem::IntegrationRule *) INSTANTIATE_ARRAY0(IntegrationRule *, IntegrationRule, 1) %include "fem/intrules.hpp" + +%feature("director") mfem::PyIntegrationRule; +%include "../common/pyintrules.hpp" + diff --git a/mfem/_ser/intrules_cut.i b/mfem/_ser/intrules_cut.i new file mode 100644 index 00000000..2a29d9fc --- /dev/null +++ b/mfem/_ser/intrules_cut.i @@ -0,0 +1,23 @@ +%module (package="mfem._ser", director="1") intrules_cut + +%{ +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +%} + +%init %{ +import_array(); +%} + +%include "exception.i" +%import "../common/exception.i" +%import "array.i" +%import "../common/numpy_int_typemap.i" +%import "mem_manager.i" + +%import "coefficient.i" + +%include "fem/intrules_cut.hpp" diff --git a/mfem/_ser/io_stream.i b/mfem/_ser/io_stream.i index c9144dbf..5c455625 100644 --- a/mfem/_ser/io_stream.i +++ b/mfem/_ser/io_stream.i @@ -6,7 +6,7 @@ #include "fstream" #include "iostream" #include "string" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" %} %include "../common/io_stream.hpp" diff --git a/mfem/_ser/istream_typemap.i b/mfem/_ser/istream_typemap.i index 1c190b25..6582ca41 100644 --- a/mfem/_ser/istream_typemap.i +++ b/mfem/_ser/istream_typemap.i @@ -4,7 +4,7 @@ %typemap(in) std::istream& (boost_ifdstream *stream=NULL) { FILE *f=PyFile_AsFile($input); // Verify that this returns NULL for non-files if (!f) { - SWIG_Error(SWIG_TypeError, "File object expected."); + SWIG_Error(SWIG_TypeError, "File object expected."); SWIG_fail; } else { diff --git a/mfem/_ser/linearform.i b/mfem/_ser/linearform.i index 2f617ea7..53be6127 100644 --- a/mfem/_ser/linearform.i +++ b/mfem/_ser/linearform.i @@ -1,12 +1,5 @@ %module(package="mfem._ser", directors="1") linearform %{ -#include "fem/fem.hpp" -#include "fem/fe_coll.hpp" -#include "fem/fespace.hpp" -#include "fem/eltrans.hpp" -#include "fem/coefficient.hpp" -#include "fem/linearform.hpp" -#include "fem/intrules.hpp" #include #include #include @@ -14,9 +7,12 @@ #include #include #include +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pylininteg.hpp" %} %init %{ @@ -39,29 +35,29 @@ import_array(); //%import "fem/fespace.hpp //%include "fem/coefficient.hpp" -namespace mfem { +namespace mfem { %pythonprepend LinearForm::AddDomainIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] lfi = args[0] self._integrators.append(lfi) - lfi.thisown=0 + lfi.thisown=0 %} %pythonprepend LinearForm::AddBoundaryIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] - lfi = args[0] + lfi = args[0] self._integrators.append(lfi) lfi.thisown=0 - %} + %} %pythonprepend LinearForm::AddBdrFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] lfi = args[0] self._integrators.append(lfi) - lfi.thisown=0 + lfi.thisown=0 %} %pythonprepend LinearForm::AddInteriorFaceIntegrator %{ if not hasattr(self, "_integrators"): self._integrators = [] self._integrators.append(lfi) - lfi.thisown=0 + lfi.thisown=0 %} } diff --git a/mfem/_ser/lininteg.i b/mfem/_ser/lininteg.i index fc137bb9..bba39695 100644 --- a/mfem/_ser/lininteg.i +++ b/mfem/_ser/lininteg.i @@ -7,10 +7,12 @@ #include #include #include -#include "mfem.hpp" -#include "pyoperator.hpp" +#include "mfem.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "../common/pylininteg.hpp" +#include "../common/pyintrules.hpp" +#include "numpy/arrayobject.h" %} %init %{ @@ -20,7 +22,7 @@ import_array(); %include "exception.i" %import "globals.i" - //%include "fem/coefficient.hpp" +//%include "fem/coefficient.hpp" %import "fe.i" %import "vector.i" %import "eltrans.i" @@ -33,4 +35,7 @@ import_array(); %include "fem/lininteg.hpp" +%feature("director") mfem::PyLinearFormIntegrator; +%include "../common/pylininteg.hpp" + diff --git a/mfem/_ser/matrix.i b/mfem/_ser/matrix.i index fc53228e..37834f74 100644 --- a/mfem/_ser/matrix.i +++ b/mfem/_ser/matrix.i @@ -6,9 +6,9 @@ #include #include #include "mfem.hpp" -#include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" %} %begin %{ diff --git a/mfem/_ser/mem_manager.i b/mfem/_ser/mem_manager.i index b4dd3fa4..d9130ac9 100644 --- a/mfem/_ser/mem_manager.i +++ b/mfem/_ser/mem_manager.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/mem_manager.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_ser/mesh.i b/mfem/_ser/mesh.i index 113b4b33..8c2759cd 100644 --- a/mfem/_ser/mesh.i +++ b/mfem/_ser/mesh.i @@ -11,9 +11,10 @@ #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" #include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %begin %{ diff --git a/mfem/_ser/mesh_operators.i b/mfem/_ser/mesh_operators.i index d1a3b789..3476458e 100644 --- a/mfem/_ser/mesh_operators.i +++ b/mfem/_ser/mesh_operators.i @@ -3,8 +3,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} // initialization required to return numpy array from SWIG %init %{ @@ -21,4 +22,4 @@ import_array(); %include "../common/typemap_macros.i" LIST_TO_MFEMOBJ_POINTERARRAY_IN(mfem::IntegrationRule const *irs_[], mfem::IntegrationRule *, 1) -%include "mesh/mesh_operators.hpp" +%include "mesh/mesh_operators.hpp" diff --git a/mfem/_ser/multigrid.i b/mfem/_ser/multigrid.i index 3c468c51..87fd5505 100644 --- a/mfem/_ser/multigrid.i +++ b/mfem/_ser/multigrid.i @@ -8,8 +8,10 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ import_array(); @@ -43,16 +45,16 @@ BoolArrayInput(bool); %} %pythonprepend mfem::PyGeometricMultigrid::AppendEssentialTDofs %{ if not hasattr(self, "_esss"): self._esss = [] - self._esss.append(ess) + self._esss.append(ess) ess.thisown = 0 %} %feature("shadow") mfem::PyGeometricMultigrid::_pybfs %{ - @property + @property def bfs(self): return self._forms - %} -%feature("shadow") mfem::PyGeometricMultigrid::_pyess %{ - @property + %} +%feature("shadow") mfem::PyGeometricMultigrid::_pyess %{ + @property def essentialTrueDofs(self): return self._esss %} @@ -63,9 +65,9 @@ BoolArrayInput(bool); class PyGeometricMultigrid : public GeometricMultigrid { public: - PyGeometricMultigrid(const FiniteElementSpaceHierarchy& fespaces_) + PyGeometricMultigrid(const FiniteElementSpaceHierarchy& fespaces_) : GeometricMultigrid(fespaces_){} - + void AppendBilinearForm(BilinearForm *form){ bfs.Append(form); } @@ -73,10 +75,10 @@ public: essentialTrueDofs.Append(ess); } void _pybfs(void){} - void _pyess(void){} + void _pyess(void){} }; } /* end of namespace */ %} - + diff --git a/mfem/_ser/ncmesh.i b/mfem/_ser/ncmesh.i index d2f08c3c..b0117c36 100644 --- a/mfem/_ser/ncmesh.i +++ b/mfem/_ser/ncmesh.i @@ -5,11 +5,12 @@ %{ #include #include -#include "../common/io_stream.hpp" #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/nonlinearform.i b/mfem/_ser/nonlinearform.i index 4f35dd86..8bb38a7a 100644 --- a/mfem/_ser/nonlinearform.i +++ b/mfem/_ser/nonlinearform.i @@ -1,13 +1,12 @@ %module(package="mfem._ser") nonlinearform %{ -#include "fem/estimators.hpp" -#include "fem/linearform.hpp" -#include "fem/nonlininteg.hpp" -#include "fem/nonlinearform.hpp" -#include "fem/fespace.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pynonlininteg.hpp" %} %init %{ @@ -23,38 +22,40 @@ import_array(); %include "../common/typemap_macros.i" -namespace mfem { +namespace mfem { %pythonprepend NonlinearForm::AddDomainIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] + nlfi = args[0] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend NonlinearForm::AddInteriorFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend NonlinearForm::AddBdrFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] -# self._integrators.append(nlfi) nlfi = args[0] - nlfi.thisown=0 +# self._integrators.append(nlfi) + nlfi.thisown=0 %} %pythonprepend BlockNonlinearForm::AddDomainIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] + nlfi = args[0] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend BlockNonlinearForm::AddInteriorFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] # self._integrators.append(nlfi) - nlfi.thisown=0 + nlfi.thisown=0 %} %pythonprepend BlockNonlinearForm::AddBdrFaceIntegrator %{ # if not hasattr(self, "_integrators"): self._integrators = [] -# self._integrators.append(nlfi) nlfi = args[0] - nlfi.thisown=0 +# self._integrators.append(nlfi) + nlfi.thisown=0 %} } diff --git a/mfem/_ser/nonlininteg.i b/mfem/_ser/nonlininteg.i index e23490e1..25a531df 100644 --- a/mfem/_ser/nonlininteg.i +++ b/mfem/_ser/nonlininteg.i @@ -1,9 +1,11 @@ %module(package="mfem._ser", directors="1") nonlininteg %{ -#include "mfem.hpp" +#include "mfem.hpp" #include "../common/pycoefficient.hpp" -#include "pyoperator.hpp" -using namespace mfem; +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pynonlininteg.hpp" +using namespace mfem; %} /* %init %{ @@ -13,12 +15,12 @@ import_array(); /* %exception { try { $action } - catch (Swig::DirectorException &e) { SWIG_fail; } + catch (Swig::DirectorException &e) { SWIG_fail; } //catch (...){ // SWIG_fail; //} // catch (Swig::DirectorMethodException &e) { SWIG_fail; } - // catch (std::exception &e) { SWIG_fail; } + // catch (std::exception &e) { SWIG_fail; } } */ %include "exception.i" @@ -28,6 +30,7 @@ import_array(); %import "eltrans.i" %import "../common/exception_director.i" -%feature("director") mfem::NonlinearFormIntegrator; - %include "fem/nonlininteg.hpp" + +%feature("director") mfem::PyNonlinearFormIntegrator; +%include "../common/pynonlininteg.hpp" diff --git a/mfem/_ser/ode.i b/mfem/_ser/ode.i index bd5348e5..d1802f30 100644 --- a/mfem/_ser/ode.i +++ b/mfem/_ser/ode.i @@ -2,8 +2,8 @@ %{ #include "mfem.hpp" #include "linalg/ode.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" %} diff --git a/mfem/_ser/operators.i b/mfem/_ser/operators.i index a34e6ce3..7327220a 100644 --- a/mfem/_ser/operators.i +++ b/mfem/_ser/operators.i @@ -4,11 +4,11 @@ %{ #include -#include +#include #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" #include "numpy/arrayobject.h" %} @@ -82,7 +82,7 @@ INSTANTIATE_ARRAY0(Solver *, Solver, 1) %include "linalg/operator.hpp" -%include "pyoperator.hpp" +%include "../common/pyoperator.hpp" %pythoncode %{ class PyOperator(PyOperatorBase): @@ -94,15 +94,15 @@ class PyOperator(PyOperatorBase): raise NotImplementedError('you must specify this method') class PyTimeDependentOperator(PyTimeDependentOperatorBase): - def __init__(self, *args): + def __init__(self, *args): PyTimeDependentOperatorBase.__init__(self, *args) def _EvalMult(self, x): return self.EvalMult(x.GetDataArray()) def EvalMult(self, x): raise NotImplementedError('you must specify this method') - + %} - + /* void PrintMatlab(std::ostream & out, int n = 0, int m = 0) const; */ diff --git a/mfem/_ser/ostream_typemap.i b/mfem/_ser/ostream_typemap.i index f8d16125..f8c35a30 100644 --- a/mfem/_ser/ostream_typemap.i +++ b/mfem/_ser/ostream_typemap.i @@ -36,7 +36,7 @@ SWIG_fail; } else { - std::ofstream out(filename); + std::ofstream out(filename); $1 = &out; } } diff --git a/mfem/_ser/point.i b/mfem/_ser/point.i index 4c6c6ae0..9608f066 100644 --- a/mfem/_ser/point.i +++ b/mfem/_ser/point.i @@ -4,8 +4,9 @@ %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/pyoperator.hpp b/mfem/_ser/pyoperator.hpp deleted file mode 100644 index d6e78549..00000000 --- a/mfem/_ser/pyoperator.hpp +++ /dev/null @@ -1,22 +0,0 @@ -#include "linalg/operator.hpp" - -namespace mfem{ -class PyOperatorBase : public Operator - { - public: - explicit PyOperatorBase(int s = 0): Operator(s){} - PyOperatorBase(int h, int w) : Operator(h, w){} - virtual void Mult(const Vector &x, Vector &y) const; - virtual Vector &_EvalMult(const Vector &) const = 0; - virtual ~PyOperatorBase() {} - }; - class PyTimeDependentOperatorBase : public TimeDependentOperator - { - public: - explicit PyTimeDependentOperatorBase(int n = 0, double _t = 0.0): TimeDependentOperator(n, _t){} - PyTimeDependentOperatorBase(int h, int w, double _t=0.0) : TimeDependentOperator(h, w, _t){} - virtual void Mult(const Vector &x, Vector &y) const; - virtual Vector &_EvalMult(const Vector &) const = 0; - virtual ~PyTimeDependentOperatorBase() {} - }; -} diff --git a/mfem/_ser/qfunction.i b/mfem/_ser/qfunction.i index 62139aef..7e9fbef7 100644 --- a/mfem/_ser/qfunction.i +++ b/mfem/_ser/qfunction.i @@ -1,10 +1,11 @@ %module(package="mfem._ser") qfunction %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_ser/qspace.i b/mfem/_ser/qspace.i index 9e8c0e63..ef69d2b0 100644 --- a/mfem/_ser/qspace.i +++ b/mfem/_ser/qspace.i @@ -1,10 +1,11 @@ %module(package="mfem._ser") qspace %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_ser/quadinterpolator.i b/mfem/_ser/quadinterpolator.i index 642973bf..9813ea3b 100644 --- a/mfem/_ser/quadinterpolator.i +++ b/mfem/_ser/quadinterpolator.i @@ -1,10 +1,11 @@ %module(package="mfem._ser") quadinterpolator %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_ser/quadinterpolator_face.i b/mfem/_ser/quadinterpolator_face.i index 8d8648fd..c40d1ecb 100644 --- a/mfem/_ser/quadinterpolator_face.i +++ b/mfem/_ser/quadinterpolator_face.i @@ -1,10 +1,11 @@ %module(package="mfem._ser") quadinterpolator_face %{ #include "mfem.hpp" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_ser/quadrilateral.i b/mfem/_ser/quadrilateral.i index b14cdce7..667bef52 100644 --- a/mfem/_ser/quadrilateral.i +++ b/mfem/_ser/quadrilateral.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") quadrilateral %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/restriction.i b/mfem/_ser/restriction.i index fc0c8fe1..b8f2999c 100644 --- a/mfem/_ser/restriction.i +++ b/mfem/_ser/restriction.i @@ -1,10 +1,10 @@ %module(package="mfem._ser") restriction %{ #include "mfem.hpp" -#include "fem/restriction.hpp" -#include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/segment.i b/mfem/_ser/segment.i index d72c8379..900eed0a 100644 --- a/mfem/_ser/segment.i +++ b/mfem/_ser/segment.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") segment %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/sets.i b/mfem/_ser/sets.i index dd110132..9b69004a 100644 --- a/mfem/_ser/sets.i +++ b/mfem/_ser/sets.i @@ -1,7 +1,7 @@ %module(package="mfem._ser") sets %{ #include "general/sets.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_ser/setup.py b/mfem/_ser/setup.py index b0538f46..d7f2a7c3 100644 --- a/mfem/_ser/setup.py +++ b/mfem/_ser/setup.py @@ -62,14 +62,14 @@ def get_extensions(): libraries = ['mfem'] # remove current directory from path - print("__file__", os.path.abspath(__file__)) + #print("__file__", os.path.abspath(__file__)) if '' in sys.path: sys.path.remove('') items = [x for x in sys.path if os.path.abspath( x) == os.path.dirname(os.path.abspath(__file__))] for x in items: sys.path.remove(x) - print("sys path", sys.path) + #print("sys path", sys.path) # this forces to use compiler written in setup_local.py if cc_ser != '': @@ -92,7 +92,8 @@ def get_extensions(): "linearform", "vector", "lininteg", "complex_operator", "complex_fem", "gridfunc", "hybridization", "bilinearform", - "bilininteg", "intrules", "sparsemat", "densemat", + "bilininteg", "intrules", "intrules_cut", + "sparsemat", "densemat", "solvers", "estimators", "mesh_operators", "ode", "sparsesmoothers", "matrix", "operators", "ncmesh", "eltrans", "geom", @@ -101,7 +102,7 @@ def get_extensions(): "transfer", "std_vectors", "tmop", "tmop_amr", "tmop_tools", "qspace", "qfunction", "quadinterpolator", "quadinterpolator_face", - "submesh", "transfermap"] + "submesh", "transfermap", "staticcond", "sidredatacollection"] if add_cuda == '1': from setup_local import cudainc @@ -124,6 +125,8 @@ def get_extensions(): tpl_include = [] for x in mfemstpl.split(' '): if x.startswith("-I"): + if x.find("MacOS") != -1 and x.find(".sdk") != -1: + continue tpl_include.append(x[2:]) include_dirs.extend(tpl_include) diff --git a/mfem/_ser/sidredatacollection.i b/mfem/_ser/sidredatacollection.i new file mode 100644 index 00000000..9eedaef5 --- /dev/null +++ b/mfem/_ser/sidredatacollection.i @@ -0,0 +1,17 @@ +%module(package="mfem._ser") sidredatacollection +%{ +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +%} + +%init %{ +import_array(); +%} + +%include "exception.i" +%import "datacollection.i" + +%include "fem/sidredatacollection.hpp" diff --git a/mfem/_ser/socketstream.i b/mfem/_ser/socketstream.i index 688f14d1..2fc0e336 100644 --- a/mfem/_ser/socketstream.i +++ b/mfem/_ser/socketstream.i @@ -4,10 +4,11 @@ %{ #include #include "mfem.hpp" -#include "pyoperator.hpp" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" -#include "numpy/arrayobject.h" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ @@ -25,19 +26,19 @@ import_array(); %extend mfem::socketstream{ int precision(const int p) { - return self->precision(p); + return self->precision(p); } int precision() - { + { return self->precision(); } void send_solution(const mfem::Mesh &mesh, - const mfem::GridFunction &gf) + const mfem::GridFunction &gf) { *self << "solution\n" << mesh << gf << std::flush; } void send_text(const char ostr[]) - { + { *self << ostr << std::endl; } void flush() @@ -48,24 +49,24 @@ import_array(); { return self->std::iostream::good(); } - + mfem::socketstream& __lshift__(const char ostr[]) - { + { *self << ostr; return *self; } mfem::socketstream& __lshift__(const int x) - { + { *self << x; return *self; } mfem::socketstream& __lshift__(const mfem::Mesh &mesh) - { + { *self << mesh; return *self; } mfem::socketstream& __lshift__(const mfem::GridFunction &gf) - { + { *self << gf; return *self; } @@ -73,7 +74,7 @@ import_array(); { *self << std::endl; return *self; - } - - -} + } + + +} diff --git a/mfem/_ser/solvers.i b/mfem/_ser/solvers.i index c8c8f724..e538bf39 100644 --- a/mfem/_ser/solvers.i +++ b/mfem/_ser/solvers.i @@ -1,11 +1,11 @@ %module(package="mfem._ser", directors="1") solvers %{ -#include "linalg/handle.hpp" +#include "linalg/handle.hpp" #include "linalg/matrix.hpp" #include "linalg/sparsemat.hpp" #include "linalg/solvers.hpp" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pysolvers.hpp" #include "numpy/arrayobject.h" %} @@ -65,14 +65,14 @@ namespace mfem{ mfem_error("Mult is not implemented"); } void PyIterativeSolver::MultTranspose(const Vector &b, Vector &x) const{ - mfem_error("MultTranspose is not implemented"); + mfem_error("MultTranspose is not implemented"); } void PyIterativeSolver::SetPreconditioner(Solver &pr){ - mfem_error("SetPreconditioner is not implemented"); + mfem_error("SetPreconditioner is not implemented"); } /// Also calls SetOperator for the preconditioner if there is one void PyIterativeSolver::SetOperator(const Operator &op){ - mfem_error("SetOperator is not implemented"); + mfem_error("SetOperator is not implemented"); } } /* end of namespace */ %} diff --git a/mfem/_ser/sort_pairs.i b/mfem/_ser/sort_pairs.i index 54251a8f..a2c15f6d 100644 --- a/mfem/_ser/sort_pairs.i +++ b/mfem/_ser/sort_pairs.i @@ -2,7 +2,7 @@ %{ #include "mfem.hpp" #include "general/globals.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" %} %init %{ diff --git a/mfem/_ser/sparsemat.i b/mfem/_ser/sparsemat.i index 2766121f..680404a9 100644 --- a/mfem/_ser/sparsemat.i +++ b/mfem/_ser/sparsemat.i @@ -1,15 +1,15 @@ %module (package="mfem._ser") sparsemat %{ -#include +#include #include #include #include #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/io_stream.hpp" -using namespace mfem; +using namespace mfem; %} // initialization required to return numpy array from SWIG %begin %{ @@ -45,7 +45,7 @@ OSTREAM_TYPEMAP(std::ostream&) %} %pythonprepend mfem::SparseMatrix::SparseMatrix %{ -import numpy as np +import numpy as np from scipy.sparse import csr_matrix if len(args) == 1 and isinstance(args[0], csr_matrix): csr = args[0] @@ -65,9 +65,9 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): self._i_data = i self._j_data = j self._d_data = data - + return -%} +%} // RAP_P, RAP_R replaces RAP, since RAP has two definition one accept // pointer and the other accept reference. From Python, two @@ -77,8 +77,8 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): const mfem::SparseMatrix &R, mfem::SparseMatrix *ORAP){ return RAP(A, R, ORAP); - } - + } + mfem::SparseMatrix *RAP_R(const mfem::SparseMatrix &Rt, const mfem::SparseMatrix &A, const mfem::SparseMatrix &P){ @@ -88,14 +88,14 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): mfem::SparseMatrix &OperatorPtr2SparseMatrix(mfem::OperatorPtr op) { return dynamic_cast(* op); } - + mfem::SparseMatrix &OperatorHandle2SparseMatrix(mfem::OperatorHandle op) { return dynamic_cast(* op); } %} /* - support numpy array input to + support numpy array input to SparseMatrix(int *i, int *j, double *data, int m, int n); allows to use numpy array to call this */ @@ -118,11 +118,11 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): //PyArray_CLEARFLAGS(tmp_arr1_, NPY_ARRAY_OWNDATA); //PyArray_CLEARFLAGS(tmp_arr2_, NPY_ARRAY_OWNDATA); // - PyArray_CLEARFLAGS(tmp_arr3_, NPY_ARRAY_OWNDATA); + PyArray_CLEARFLAGS(tmp_arr3_, NPY_ARRAY_OWNDATA); } %typemap(freearg) (int *i, int *j, double *data, int m, int n){ //Py_XDECREF(tmp_arr1_$argnum); Dont do this.. We set OwnsGraph and OwnsData to Fase in Python - //Py_XDECREF(tmp_arr2_$argnum); + //Py_XDECREF(tmp_arr2_$argnum); //Py_XDECREF(tmp_arr3_$argnum); } @@ -137,7 +137,7 @@ if len(args) == 1 and isinstance(args[0], csr_matrix): if (!PyArray_Check(PyList_GetItem($input,2))) $1 = 0; if (!PyInt_Check(PyList_GetItem($input,3))) $1 = 0; if (!PyInt_Check(PyList_GetItem($input,4))) $1 = 0; - } else $1 = 0; + } else $1 = 0; } } @@ -161,7 +161,7 @@ PyObject* GetJArray(void) const{ } PyObject* GetDataArray(void) const{ const int * I = self->GetI(); - const double * A = self->GetData(); + const double * A = self->GetData(); int L = self->Size(); npy_intp dims[] = {I[L]}; return PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, (void *)A); diff --git a/mfem/_ser/sparsesmoothers.i b/mfem/_ser/sparsesmoothers.i index b77471ac..0b9826aa 100644 --- a/mfem/_ser/sparsesmoothers.i +++ b/mfem/_ser/sparsesmoothers.i @@ -1,8 +1,8 @@ %module(package="mfem._ser") sparsesmoothers %{ #include "linalg/sparsesmoothers.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "numpy/arrayobject.h" %} %init %{ @@ -23,7 +23,7 @@ import_array(); /* %extend mfem::SparseSmoother{ // void mfem::SparseSmoother::SetOperator(const SparseMatrix &a) { - void SetOperator(mfem::SparseMatrix &a) { + void SetOperator(mfem::SparseMatrix &a) { std::cout << "this is called\n"; std::cout << std::to_string(a.Height()) << "\n"; mfem::SparseMatrix *b = new mfem::SparseMatrix(a); @@ -35,4 +35,4 @@ import_array(); - + diff --git a/mfem/_ser/stable3d.i b/mfem/_ser/stable3d.i index 036b6b11..522318e4 100644 --- a/mfem/_ser/stable3d.i +++ b/mfem/_ser/stable3d.i @@ -5,9 +5,10 @@ %{ #include #include "mfem.hpp" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %begin %{ diff --git a/mfem/_ser/staticcond.i b/mfem/_ser/staticcond.i new file mode 100644 index 00000000..5f5efe18 --- /dev/null +++ b/mfem/_ser/staticcond.i @@ -0,0 +1,17 @@ +%module(package="mfem._ser") staticcond +%{ +#include "mfem.hpp" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +%} + +%init %{ +import_array(); +%} + +%include "exception.i" +%import "fespace.i" + +%include "fem/staticcond.hpp" diff --git a/mfem/_ser/std_vectors.i b/mfem/_ser/std_vectors.i index 3862a5de..ebb80685 100644 --- a/mfem/_ser/std_vectors.i +++ b/mfem/_ser/std_vectors.i @@ -7,9 +7,9 @@ // in a module which imports i file where std_vector.i is imported. %{ #include -#include "mfem.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" #include "../common/io_stream.hpp" %} @@ -33,4 +33,4 @@ import_array(); %template(vector_SparseMatrix) std::vector; - + diff --git a/mfem/_ser/submesh.i b/mfem/_ser/submesh.i index bcb27487..152bb902 100644 --- a/mfem/_ser/submesh.i +++ b/mfem/_ser/submesh.i @@ -5,8 +5,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_ser/symmat.i b/mfem/_ser/symmat.i index 5c2e45bc..cc793fac 100644 --- a/mfem/_ser/symmat.i +++ b/mfem/_ser/symmat.i @@ -3,8 +3,8 @@ #include "mfem.hpp" #include "linalg/symmat.hpp" #include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" -#include "pyoperator.hpp" +#include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" %} %init %{ diff --git a/mfem/_ser/table.i b/mfem/_ser/table.i index 25c88418..a984ee79 100644 --- a/mfem/_ser/table.i +++ b/mfem/_ser/table.i @@ -3,11 +3,11 @@ %feature("autodoc", "1"); %{ -#include +#include #include #include "mfem.hpp" -#include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" +#include "numpy/arrayobject.h" +#include "../common/io_stream.hpp" #include "general/table.hpp" %} diff --git a/mfem/_ser/tetrahedron.i b/mfem/_ser/tetrahedron.i index d6bd9f04..7be00018 100644 --- a/mfem/_ser/tetrahedron.i +++ b/mfem/_ser/tetrahedron.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") tetrahedron %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/tmop.i b/mfem/_ser/tmop.i index c7503893..6d0152b9 100644 --- a/mfem/_ser/tmop.i +++ b/mfem/_ser/tmop.i @@ -2,8 +2,11 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" +#include "../common/pynonlininteg.hpp" %} %init %{ @@ -22,7 +25,7 @@ LIST_TO_MFEMOBJ_BOOLARRAY_IN(const mfem::Array& ) %import "../common/array_instantiation_macro.i" IGNORE_ARRAY_METHODS(mfem::TMOP_Integrator *) -INSTANTIATE_ARRAY0(TMOP_Integrator *, TMOP_Integrator, 1) +INSTANTIATE_ARRAY0(TMOP_Integrator *, TMOP_Integrator, 1) /* destructor handles freeing evaluator */ %pythonappend mfem::DiscreteAdaptTC::SetAdaptivityEvaluator %{ diff --git a/mfem/_ser/tmop_amr.i b/mfem/_ser/tmop_amr.i index 66842141..31094e31 100644 --- a/mfem/_ser/tmop_amr.i +++ b/mfem/_ser/tmop_amr.i @@ -2,8 +2,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/tmop_tools.i b/mfem/_ser/tmop_tools.i index 5cce019c..3e4cf2e5 100644 --- a/mfem/_ser/tmop_tools.i +++ b/mfem/_ser/tmop_tools.i @@ -2,9 +2,10 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" +#include "../common/pyoperator.hpp" #include "../common/pycoefficient.hpp" -#include "../common/pysolvers.hpp" +#include "../common/pysolvers.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/transfer.i b/mfem/_ser/transfer.i index 76d78afc..b243bbd8 100644 --- a/mfem/_ser/transfer.i +++ b/mfem/_ser/transfer.i @@ -3,12 +3,12 @@ %feature("autodoc", "1"); %{ -#include "mfem.hpp" -#include "mesh/vertex.hpp" +#include "mfem.hpp" #include "numpy/arrayobject.h" -#include "fem/transfer.hpp" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" +#include "../common/pybilininteg.hpp" %} %init %{ @@ -20,6 +20,6 @@ import_array(); %import "fespace.i" %include "../common/exception.i" -%import "pyoperator.hpp" +//%import "../common/pyoperator.hpp" %include "fem/transfer.hpp" diff --git a/mfem/_ser/transfermap.i b/mfem/_ser/transfermap.i index 05803c88..acf0db6a 100644 --- a/mfem/_ser/transfermap.i +++ b/mfem/_ser/transfermap.i @@ -5,8 +5,9 @@ %{ #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "pyoperator.hpp" -#include "../common/pycoefficient.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pycoefficient.hpp" +#include "../common/pyintrules.hpp" %} %include "../common/existing_mfem_headers.i" diff --git a/mfem/_ser/triangle.i b/mfem/_ser/triangle.i index ca4f4551..3259565f 100644 --- a/mfem/_ser/triangle.i +++ b/mfem/_ser/triangle.i @@ -1,8 +1,9 @@ %module(package="mfem._ser") triangle %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/vector.i b/mfem/_ser/vector.i index 6c8a3208..ec1a34a8 100644 --- a/mfem/_ser/vector.i +++ b/mfem/_ser/vector.i @@ -6,7 +6,7 @@ %module(package="mfem._ser") vector %feature("autodoc", "1"); %{ -#include "linalg/vector.hpp" +#include "linalg/vector.hpp" #include #include #include @@ -16,7 +16,7 @@ #include #include "mfem.hpp" #include "numpy/arrayobject.h" -#include "../common/io_stream.hpp" +#include "../common/io_stream.hpp" %} // initialization required to return numpy array from SWIG @@ -50,13 +50,13 @@ from numpy import ndarray, ascontiguousarray keep_link = False own_data = False if len(args) == 1: - if isinstance(args[0], list): + if isinstance(args[0], list): args = (args[0], len(args[0])) own_data = True elif isinstance(args[0], ndarray): if args[0].dtype != 'float64': raise ValueError('Must be float64 array ' + str(args[0].dtype) + - ' is given') + ' is given') else: args = (ascontiguousarray(args[0]), args[0].shape[0]) # in this case, args[0] need to be maintained @@ -75,28 +75,28 @@ if own_data: def __iadd__(self, v): ret = _vector.Vector___iadd__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self %} %feature("shadow") mfem::Vector::operator-= %{ def __isub__(self, v): ret = _vector.Vector___isub__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self -%} +%} %feature("shadow") mfem::Vector::operator*= %{ def __imul__(self, v): ret = _vector.Vector___imul__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self -%} +%} %feature("shadow") mfem::Vector::operator/= %{ def __itruediv__(self, v): ret = _vector.Vector___itruediv__(self, v) #ret.thisown = self.thisown - ret.thisown = 0 + ret.thisown = 0 return self %} //rename(Assign) mfem::Vector::operator=; @@ -109,15 +109,15 @@ if len(args) == 1: raise ValueError('Must be float64 array ' + str(args[0].dtype) + ' is given') elif args[0].ndim != 1: - raise ValueError('Ndim must be one') + raise ValueError('Ndim must be one') elif args[0].shape[0] != self.Size(): raise ValueError('Length does not match') else: args = (ascontiguousarray(args[0]),) elif isinstance(args[0], tuple): - args = (array(args[0], dtype = float),) - elif isinstance(args[0], list): - args = (array(args[0], dtype = float),) + args = (array(args[0], dtype = float),) + elif isinstance(args[0], list): + args = (array(args[0], dtype = float),) else: pass %} @@ -174,10 +174,10 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) %include "linalg/vector.hpp" %extend mfem::Vector { - /* define Assign as a replacement of = operator */ + /* define Assign as a replacement of = operator */ Vector(const mfem::Vector &v, int offset, int size){ mfem::Vector *vec; - vec = new mfem::Vector(v.GetData() + offset, size); + vec = new mfem::Vector(v.GetData() + offset, size); return vec; } void Assign(const double v) { @@ -190,7 +190,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) /* note that these error does not raise error in python type check is actually done in wrapper layer */ PyArrayObject *param0 = reinterpret_cast(param); - + if (!PyArray_Check(param0)){ PyErr_SetString(PyExc_ValueError, "Input data must be ndarray"); return; @@ -205,25 +205,25 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) PyErr_SetString(PyExc_ValueError, "Input data NDIM must be one"); return ; } - npy_intp *shape = PyArray_DIMS(param0); + npy_intp *shape = PyArray_DIMS(param0); int len = self->Size(); - if (shape[0] != len){ + if (shape[0] != len){ PyErr_SetString(PyExc_ValueError, "input data length does not match"); return ; - } + } (* self) = (double *) PyArray_DATA(param0); } void __setitem__(int i, const double v) { - int len = self->Size(); - if (i >= 0){ + int len = self->Size(); + if (i >= 0){ (* self)(i) = v; } else { (* self)(len+i) = v; } } PyObject* __getitem__(PyObject* param) { - int len = self->Size(); + int len = self->Size(); if (PySlice_Check(param)) { long start = 0, stop = 0, step = 0, slicelength = 0; int check; @@ -238,12 +238,12 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) if (check == -1) { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Vector failed."); - return NULL; + return NULL; } if (step == 1) { mfem::Vector *vec; vec = new mfem::Vector(self->GetData() + start, slicelength); - return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Vector *), 1); + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Vector *), 1); } else { mfem::Vector *vec; vec = new mfem::Vector(slicelength); @@ -261,7 +261,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) long idx = PyInt_AsLong(param); if (PyErr_Occurred()) { PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); - return NULL; + return NULL; } if ((idx >= len) && (idx >= -len-1)){ PyErr_SetString(PyExc_IndexError, "Index must be < Size (counting forward) or > -Size-1 (counting backward)"); @@ -275,23 +275,23 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) } } PyObject* GetDataArray(void) const{ - double * A = self->GetData(); + double * A = self->GetData(); int L = self->Size(); npy_intp dims[] = {L}; return PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, A); } - + PyObject* WriteToStream(PyObject* StringIO, int width=8) const { PyObject* module = PyImport_ImportModule("io"); if (!module){ PyErr_SetString(PyExc_RuntimeError, "Can not load io module"); return (PyObject *) NULL; - } + } PyObject* cls = PyObject_GetAttrString(module, "StringIO"); if (!cls){ PyErr_SetString(PyExc_RuntimeError, "Can not load StringIO"); return (PyObject *) NULL; - } + } int check = PyObject_IsInstance(StringIO, cls); Py_DECREF(module); if (! check){ @@ -299,7 +299,7 @@ INSTANTIATE_ARRAY0(Vector *, Vector, 1) return (PyObject *) NULL; } std::ostringstream stream; - self->Print(stream, width); + self->Print(stream, width); std::string str = stream.str(); const char* s = str.c_str(); const int n = str.length(); @@ -322,6 +322,6 @@ linalg/vector.hpp: void Print_HYPRE(std::ostream &out) const; #ifndef SWIGIMPORTED OSTREAM_ADD_DEFAULT_FILE(Vector, Print) OSTREAM_ADD_DEFAULT_STDOUT_FILE(Vector, Print_HYPRE) -#endif +#endif + - diff --git a/mfem/_ser/vertex.i b/mfem/_ser/vertex.i index c9834933..1653b1f9 100644 --- a/mfem/_ser/vertex.i +++ b/mfem/_ser/vertex.i @@ -1,9 +1,10 @@ %module(package="mfem._ser") vertex - + %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/_ser/vtk.i b/mfem/_ser/vtk.i index 679e2d49..cfb66d56 100644 --- a/mfem/_ser/vtk.i +++ b/mfem/_ser/vtk.i @@ -1,9 +1,10 @@ %module(package="mfem._ser") vtk %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" #include "../common/io_stream.hpp" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %begin %{ #define PY_SSIZE_T_CLEAN diff --git a/mfem/_ser/wedge.i b/mfem/_ser/wedge.i index f157a567..902c0611 100644 --- a/mfem/_ser/wedge.i +++ b/mfem/_ser/wedge.i @@ -2,8 +2,9 @@ %{ #include "mfem.hpp" -#include "pyoperator.hpp" -#include "numpy/arrayobject.h" +#include "numpy/arrayobject.h" +#include "../common/pyoperator.hpp" +#include "../common/pyintrules.hpp" %} %init %{ diff --git a/mfem/common/array_instantiation_macro.i b/mfem/common/array_instantiation_macro.i index 8ac64b35..c7feb0f2 100644 --- a/mfem/common/array_instantiation_macro.i +++ b/mfem/common/array_instantiation_macro.i @@ -5,207 +5,298 @@ %template(##YYY##Array) mfem::Array; #endif %extend mfem::Array { - + PyObject * __getitem__(PyObject* param) { - int len = self->Size(); + int len = self->Size(); if (PySlice_Check(param)) { long start = 0, stop = 0, step = 0, slicelength = 0; int check; - //%#ifdef TARGET_PY3 - check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, - &slicelength); + //%#ifdef TARGET_PY3 + check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, + &slicelength); //%#else - //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, - // &slicelength); - //%#endif + //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, + // &slicelength); + //%#endif - if (check == -1) { + if (check == -1) { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array failed."); - return NULL; - } - if (step == 1) { - mfem::Array *vec; - vec = new mfem::Array(self->GetData() + start, slicelength); - return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); - } else { + return NULL; + } + if (step == 1) { + mfem::Array *vec; + vec = new mfem::Array(self->GetData() + start, slicelength); + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); + } else { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array with stride>1 not supported."); - return NULL; - } + return NULL; + } } else { PyErr_Clear(); long idx = PyInt_AsLong(param); if (PyErr_Occurred()) { PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); - return NULL; + return NULL; } int own = 0; - swig_type_info *ty = $descriptor(const mfem::YYY *); + swig_type_info *ty = $descriptor(const mfem::YYY *); #if USEPTR == 1 - if (idx >= 0){ + if (idx >= 0){ return SWIG_NewPointerObj(SWIG_as_voidptr((self->operator[](idx))), ty, own); } else { - return SWIG_NewPointerObj(SWIG_as_voidptr((self->operator[](len+idx))), ty, own); - } + return SWIG_NewPointerObj(SWIG_as_voidptr((self->operator[](len+idx))), ty, own); + } #else if (idx >= 0){ return SWIG_NewPointerObj(SWIG_as_voidptr(&(self->operator[](idx))), ty, own); } else { - return SWIG_NewPointerObj(SWIG_as_voidptr(&(self->operator[](len+idx))), ty, own); - } - #endif + return SWIG_NewPointerObj(SWIG_as_voidptr(&(self->operator[](len+idx))), ty, own); + } + #endif } } }; %enddef %define INSTANTIATE_ARRAY(XXX) -INSTANTIATE_ARRAY0(XXX, XXX, 0) +INSTANTIATE_ARRAY0(XXX, XXX, 0) %enddef %define INSTANTIATE_ARRAY_INT %template(intArray) mfem::Array; -%extend mfem::Array { +%extend mfem::Array { PyObject * __getitem__(PyObject* param) { - int len = self->Size(); + int len = self->Size(); if (PySlice_Check(param)) { long start = 0, stop = 0, step = 0, slicelength = 0; int check; - //%#ifdef TARGET_PY3 - check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, - &slicelength); + //%#ifdef TARGET_PY3 + check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, + &slicelength); //%#else - //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, - // &slicelength); + //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, + // &slicelength); //%#endif - if (check == -1) { + if (check == -1) { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array failed."); - return NULL; - } - if (step == 1) { + return NULL; + } + if (step == 1) { mfem::Array *vec; vec = new mfem::Array(self->GetData() + start, slicelength); - return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); - } else { + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); + } else { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array with stride>1 not supported."); - return NULL; - } + return NULL; + } } else { PyErr_Clear(); long idx = PyInt_AsLong(param); if (PyErr_Occurred()) { PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); - return NULL; + return NULL; } if (idx >= 0){ return PyLong_FromLong(self->operator[](idx)); } else { return PyLong_FromLong(self->operator[](len+idx)); - } + } } } + PyObject* GetDataArray(void) const{ + const int * A = self->GetData(); + int L = self->Size(); + npy_intp dims[] = {L}; + if (sizeof(int) == 4){ + return PyArray_SimpleNewFromData(1, dims, NPY_INT32, (void *)A); + } else { + // sizeof(int) == 8: + return PyArray_SimpleNewFromData(1, dims, NPY_INT64, (void *)A); + } + } + }; %enddef + %define INSTANTIATE_ARRAY_DOUBLE %template(doubleArray) mfem::Array; -%extend mfem::Array { +%extend mfem::Array { PyObject * __getitem__(PyObject* param) { - int len = self->Size(); + int len = self->Size(); if (PySlice_Check(param)) { long start = 0, stop = 0, step = 0, slicelength = 0; int check; - //%#ifdef TARGET_PY3 - check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, - &slicelength); + //%#ifdef TARGET_PY3 + check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, + &slicelength); //%#else - //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, - // &slicelength); - //%#endif + //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, + // &slicelength); + //%#endif - if (check == -1) { + if (check == -1) { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array failed."); - return NULL; - } - if (step == 1) { + return NULL; + } + if (step == 1) { mfem::Array *vec; vec = new mfem::Array(self->GetData() + start, slicelength); - return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); - } else { + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); + } else { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array with stride>1 not supported."); - return NULL; - } + return NULL; + } } else { PyErr_Clear(); long idx = PyInt_AsLong(param); if (PyErr_Occurred()) { PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); - return NULL; + return NULL; } if (idx >= 0){ return PyFloat_FromDouble(self->operator[](idx)); } else { return PyFloat_FromDouble(self->operator[](len+idx)); - } + } } } + PyObject* GetDataArray(void) const{ + const double * A = self->GetData(); + int L = self->Size(); + npy_intp dims[] = {L}; + return PyArray_SimpleNewFromData(1, dims, NPY_FLOAT64, (void *)A); + } }; %enddef - + %define INSTANTIATE_ARRAY_BOOL %template(boolArray) mfem::Array; -%extend mfem::Array { +%extend mfem::Array { PyObject * __getitem__(PyObject* param) { - int len = self->Size(); + int len = self->Size(); if (PySlice_Check(param)) { long start = 0, stop = 0, step = 0, slicelength = 0; int check; - //%#ifdef TARGET_PY3 - check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, - &slicelength); + //%#ifdef TARGET_PY3 + check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, + &slicelength); //%#else - //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, - // &slicelength); - //%#endif + //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, + // &slicelength); + //%#endif - if (check == -1) { + if (check == -1) { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array failed."); - return NULL; - } - if (step == 1) { + return NULL; + } + if (step == 1) { mfem::Array *vec; vec = new mfem::Array(self->GetData() + start, slicelength); - return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); - } else { + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); + } else { PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array with stride>1 not supported."); - return NULL; - } + return NULL; + } + } else { + PyErr_Clear(); + long idx = PyInt_AsLong(param); + if (PyErr_Occurred()) { + PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); + return NULL; + } + if (idx >= 0){ + if (self->operator[](idx)){ + return Py_True; + } else { + return Py_False; + } + } else { + if (self->operator[](len+idx)){ + return Py_True; + } else { + return Py_False; + } + } + } + } + PyObject* GetDataArray(void) const{ + const bool* A = self->GetData(); + int L = self->Size(); + npy_intp dims[] = {L}; + return PyArray_SimpleNewFromData(1, dims, NPY_BOOL, (void *)A); + } + }; +%enddef + +// tool to deffine mfem::Array returining elements using numpy Scalar + // mfem::Array(unsigned int) -> uintArray + // NP_TYPE is things like NPY_FLOAT32 +%define INSTANTIATE_ARRAY_NUMPYARRAY(XXX, YYY, NP_TYPE) +%template(##XXX##Array) mfem::Array; +%extend mfem::Array { + PyObject * __getitem__(PyObject* param) { + int len = self->Size(); + if (PySlice_Check(param)) { + long start = 0, stop = 0, step = 0, slicelength = 0; + int check; + + //%#ifdef TARGET_PY3 + check = PySlice_GetIndicesEx(param, len, &start, &stop, &step, + &slicelength); + //%#else + //check = PySlice_GetIndicesEx((PySliceObject*)param, len, &start, &stop, &step, + // &slicelength); + //%#endif + + if (check == -1) { + PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array failed."); + return NULL; + } + if (step == 1) { + mfem::Array *vec; + vec = new mfem::Array(self->GetData() + start, slicelength); + return SWIG_NewPointerObj(SWIG_as_voidptr(vec), $descriptor(mfem::Array *), 1); + } else { + PyErr_SetString(PyExc_ValueError, "Slicing mfem::Array with stride>1 not supported."); + return NULL; + } } else { PyErr_Clear(); long idx = PyInt_AsLong(param); if (PyErr_Occurred()) { PyErr_SetString(PyExc_ValueError, "Argument must be either int or slice"); - return NULL; + return NULL; } + PyObject *np_val = NULL; + PyArray_Descr *descr = NULL; + if(! (descr = PyArray_DescrFromType(NP_TYPE))) { + PyErr_SetString(PyExc_TypeError, "Improper descriptor"); + return NULL; + } + + YYY *data_ptr; if (idx >= 0){ - if (self->operator[](idx)){ - return Py_True; - } else { - return Py_False; - } + data_ptr = &(self->operator[](idx)); } else { - if (self->operator[](len+idx)){ - return Py_True; - } else { - return Py_False; - } - } + data_ptr = &(self->operator[](idx+len)); + } + np_val = PyArray_Scalar(data_ptr, descr, NULL); + return np_val; } } + PyObject* GetDataArray(void) const{ + const YYY * A = self->GetData(); + int L = self->Size(); + npy_intp dims[] = {L}; + return PyArray_SimpleNewFromData(1, dims, NP_TYPE, (void *)A); + } + }; %enddef @@ -226,5 +317,25 @@ INSTANTIATE_ARRAY0(XXX, XXX, 0) %ignore mfem::Array::PrintGZ; %ignore mfem::Array::SaveGZ; %ignore mfem::Array::Load; +%ignore mfem::Array2D::Print; +%ignore mfem::Array2D::PrintGZ; +%ignore mfem::Array2D::SaveGZ; +%enddef + + +%define IGNORE_ARRAY_METHODS_PREMITIVE(XXX) +%ignore mfem::Array::PartialSum; +%ignore mfem::Array::Sum; +%ignore mfem::Array::IsSorted; +%ignore mfem::Array::Save; +%ignore mfem::Array::Max; +%ignore mfem::Array::Min; +%ignore mfem::Array::Print; +%ignore mfem::Array::PrintGZ; +%ignore mfem::Array::SaveGZ; +%ignore mfem::Array::Load; +%ignore mfem::Array2D::Print; +%ignore mfem::Array2D::PrintGZ; +%ignore mfem::Array2D::SaveGZ; %enddef diff --git a/mfem/common/bilininteg_ext.i b/mfem/common/bilininteg_ext.i index 7e8bfbae..b22c7f79 100644 --- a/mfem/common/bilininteg_ext.i +++ b/mfem/common/bilininteg_ext.i @@ -1,4 +1,8 @@ namespace mfem { +%pythonappend BilinearFormIntegrator::BilinearFormIntegrator %{ + self._coeff = args +%} + %pythonappend TransposeIntegrator::TransposeIntegrator %{ if own_bfi_ == 1: bfi_.thisown = 0 %} diff --git a/mfem/common/generate_lininteg_ext.py b/mfem/common/generate_lininteg_ext.py index a3879ce1..09e9d4fc 100644 --- a/mfem/common/generate_lininteg_ext.py +++ b/mfem/common/generate_lininteg_ext.py @@ -22,6 +22,8 @@ pp = " self._coeff = uD_" elif line.find("(self)") != -1: pass + elif line.find("(self, ir=None)") != -1: + pass else: print(cname) print(line) diff --git a/mfem/common/io_stream.hpp b/mfem/common/io_stream.hpp index 6c306117..edb937ec 100644 --- a/mfem/common/io_stream.hpp +++ b/mfem/common/io_stream.hpp @@ -1,3 +1,6 @@ +#ifndef PYMFEM_IO_STREAM +#define PYMFEM_IO_STREAM + namespace PyMFEM { class wFILE @@ -45,3 +48,5 @@ class wFILE }; } +#endif // PYMFEM_IO_STREAM + diff --git a/mfem/common/pybilininteg.hpp b/mfem/common/pybilininteg.hpp new file mode 100644 index 00000000..9be7c398 --- /dev/null +++ b/mfem/common/pybilininteg.hpp @@ -0,0 +1,16 @@ +#ifndef PYMFEM_PYBILININTEG +#define PYMFEM_PYBILININTEG + +#include +#include "fem/bilininteg.hpp" + +namespace mfem{ +class PyBilinearFormIntegrator : public BilinearFormIntegrator +{ +public: + PyBilinearFormIntegrator(const IntegrationRule *ir = NULL):BilinearFormIntegrator(ir){} + virtual ~PyBilinearFormIntegrator() { } +}; +} // end of namespace + +#endif //PYMFEM_PYBILININTEG diff --git a/mfem/common/pycoefficient.hpp b/mfem/common/pycoefficient.hpp index c4113a8f..daf37808 100644 --- a/mfem/common/pycoefficient.hpp +++ b/mfem/common/pycoefficient.hpp @@ -1,3 +1,6 @@ +#ifndef PYMFEM_PYCOEFFICIENT +#define PYMFEM_PYCOEFFICIENT + #include "fem/coefficient.hpp" #define assertm(exp, msg) assert(((void)msg, exp)) @@ -190,4 +193,4 @@ class MatrixNumbaCoefficient : public mfem::MatrixFunctionCoefficient, public N const mfem::IntegrationPoint &ip); }; - +#endif //PYMFEM_PYCOEFFICIENT diff --git a/mfem/common/pyintrules.hpp b/mfem/common/pyintrules.hpp new file mode 100644 index 00000000..062e5911 --- /dev/null +++ b/mfem/common/pyintrules.hpp @@ -0,0 +1,16 @@ +#ifndef PYMFEM_PYINTRULES +#define PYMFEM_PYINTRULES + +#include +#include "fem/intrules.hpp" + +namespace mfem{ +class PyIntegrationRule : public IntegrationRule +{ +public: + PyIntegrationRule():IntegrationRule(){} + virtual ~PyIntegrationRule(){} +}; +} // end of namespace + +#endif //PYMFEM_PYINTRULES diff --git a/mfem/common/pylininteg.hpp b/mfem/common/pylininteg.hpp new file mode 100644 index 00000000..b4d30897 --- /dev/null +++ b/mfem/common/pylininteg.hpp @@ -0,0 +1,17 @@ +#ifndef PYMFEM_PYLININTEG +#define PYMFEM_PYLININTEG + +#include +#include "fem/lininteg.hpp" + +namespace mfem{ +class PyLinearFormIntegrator : public LinearFormIntegrator +{ +public: + PyLinearFormIntegrator(const IntegrationRule *ir = NULL):LinearFormIntegrator(ir) {} + virtual ~PyLinearFormIntegrator() { } +}; +} // end of namespace + +#endif // PYMFEM_PYLININTEG + diff --git a/mfem/common/pynonlininteg.hpp b/mfem/common/pynonlininteg.hpp new file mode 100644 index 00000000..c940e49e --- /dev/null +++ b/mfem/common/pynonlininteg.hpp @@ -0,0 +1,17 @@ +#ifndef PYMFEM_PYNONLININTEG +#define PYMFEM_PYNONLININTEG + +#include +#include "fem/nonlininteg.hpp" + +namespace mfem{ +class PyNonlinearFormIntegrator : public NonlinearFormIntegrator +{ +public: + PyNonlinearFormIntegrator(const IntegrationRule *ir = NULL):NonlinearFormIntegrator(ir) {} + virtual ~PyNonlinearFormIntegrator() { } + +}; +} // end of namespace + +#endif //PYMFEM_PYNONLININTEG diff --git a/mfem/_par/pyoperator.hpp b/mfem/common/pyoperator.hpp similarity index 90% rename from mfem/_par/pyoperator.hpp rename to mfem/common/pyoperator.hpp index d6e78549..0e3bef5f 100644 --- a/mfem/_par/pyoperator.hpp +++ b/mfem/common/pyoperator.hpp @@ -1,3 +1,6 @@ +#ifndef PYMFEM_PYOPERATOR +#define PYMFEM_PYOPERATOR + #include "linalg/operator.hpp" namespace mfem{ @@ -20,3 +23,5 @@ class PyOperatorBase : public Operator virtual ~PyTimeDependentOperatorBase() {} }; } + +#endif // PYMFEM_PYOPERATOR diff --git a/mfem/par.py b/mfem/par.py index 514aa344..f6437a78 100644 --- a/mfem/par.py +++ b/mfem/par.py @@ -40,6 +40,7 @@ from mfem._par.bilininteg import * from mfem._par.gridfunc import * from mfem._par.intrules import * +from mfem._par.intrules_cut import * from mfem._par.fe import * from mfem._par.ode import * from mfem._par.bilinearform import * diff --git a/mfem/ser.py b/mfem/ser.py index 1a2d0267..3ff0d3ca 100644 --- a/mfem/ser.py +++ b/mfem/ser.py @@ -31,6 +31,7 @@ from mfem._ser.bilininteg import * from mfem._ser.gridfunc import * from mfem._ser.intrules import * +from mfem._ser.intrules_cut import * from mfem._ser.fe import * from mfem._ser.ode import * from mfem._ser.bilinearform import * diff --git a/setup.py b/setup.py index 0d5bef15..1123dd2a 100644 --- a/setup.py +++ b/setup.py @@ -58,9 +58,11 @@ "gklib": "https://github.com/KarypisLab/GKlib", "metis": "https://github.com/KarypisLab/METIS", } repos_sha = { - # "mfem": "2f6eb8838f8f5e8359abba0dd3434c8cc7147012", - #"mfem": "00b2a0705f647e17a1d4ffcb289adca503f28d42", # version 4.5.2 - "mfem": "962774d5ffa84ceed3bc670e52388250ee028da1", # version 4.5.2 + distsolve + # "mfem": "00b2a0705f647e17a1d4ffcb289adca503f28d42", # version 4.5.2 + # "mfem": "962774d5ffa84ceed3bc670e52388250ee028da1", # version 4.5.2 + distsolve + #"mfem": "69fbae732d5279c8d0f42c5430c4fd5656731d00", # version 4.6 + #"mfem": "8bb929c2ff86cdf2ee9bb058cc75e59acb07bb94", # doftrans simplification (Nov. 15. 2023) + "mfem": "4a45c70d1269d293266b77a3a025a9756d10ed8f", # after socket connection fix (Nov. 29 2023) "gklib": "a7f8172703cf6e999dd0710eb279bba513da4fec", "metis": "94c03a6e2d1860128c2d0675cbbb86ad4f261256", } @@ -121,9 +123,10 @@ gslibs_prefix = '' gslibp_prefix = '' gslib_only = False +mfemf_debug=False enable_suitesparse = False -suitesparse_prefix = "" +suitesparse_prefix = "/usr/" enable_lapack = False blas_libraries = "" @@ -731,6 +734,10 @@ def add_rpath(p): 'DMFEM_USE_ZLIB': '1', 'DCMAKE_CXX_FLAGS': cxx11_flag, 'DCMAKE_BUILD_WITH_INSTALL_RPATH': '1'} + + if mfem_debug: + cmake_opts['DMFEM_DEBUG'] = 'YES' + if verbose: cmake_opts['DCMAKE_VERBOSE_MAKEFILE'] = '1' @@ -1147,8 +1154,8 @@ def clean_wrapper(): def clean_so(all=None): - - command = ["python", "setup.py", "clean"] + python = sys.executable + command = [python, "setup.py", "clean"] if all == 1: command.append("--all") @@ -1236,7 +1243,7 @@ def configure_install(self): global clean_swig, run_swig, swig_only, skip_install, skip_swig global build_mfem, build_mfemp, build_parallel, build_serial - global mfem_branch, mfem_source + global mfem_branch, mfem_source, mfem_debug global build_metis, build_hypre, build_libceed, build_gslib global mfems_prefix, mfemp_prefix, metis_prefix, hypre_prefix @@ -1285,6 +1292,8 @@ def configure_install(self): clean_swig = True run_swig = True + mfem_debug = bool(self.mfem_debug) + if build_serial: build_serial = (not swig_only and not ext_only) @@ -1514,6 +1523,7 @@ class Install(_install): 'MFEM is cloned and built using the specfied branch '), ('mfem-source=', None, 'Specify mfem source location' + 'MFEM source directory. Required to run-swig '), + ('mfem-debug', None, 'Build MFME with MFEM_DEBUG enabled'), ('hypre-prefix=', None, 'Specify locaiton of hypre' + 'libHYPRE.so must exits under /lib'), ('metis-prefix=', None, 'Specify locaiton of metis' + @@ -1568,6 +1578,7 @@ def initialize_options(self): self.mfemp_prefix = '' self.mfem_source = './external/mfem' self.mfem_branch = '' + self.mfem_debug = False self.metis_prefix = '' self.hypre_prefix = '' diff --git a/test/issues/README.txt b/test/issues/README.txt new file mode 100644 index 00000000..b3b910f4 --- /dev/null +++ b/test/issues/README.txt @@ -0,0 +1,6 @@ +test issues directory + +This directtory contains routines to test issues raised in repositoriy. + +Python script is named as test_xxxx.py, where xxxx is issue number +Data set folder is named using issue number. diff --git a/test/issues/data_3960/VisIt_volume/cycle_000000.mfem_root b/test/issues/data_3960/VisIt_volume/cycle_000000.mfem_root new file mode 100755 index 00000000..a08f86d4 --- /dev/null +++ b/test/issues/data_3960/VisIt_volume/cycle_000000.mfem_root @@ -0,0 +1,29 @@ +{ + "dsets": { + "main": { + "cycle": 0, + "domains": 20, + "fields": { + "pressure": { + "path": "cycle_000000/pressure.%06d", + "tags": { + "assoc": "nodes", + "comps": "1", + "lod": "2" + } + } + }, + "mesh": { + "format": "1", + "path": "cycle_000000/pmesh.%06d", + "tags": { + "max_lods": "32", + "spatial_dim": "2", + "topo_dim": "2" + } + }, + "time": 0.00033999721438235294, + "time_step": 0 + } + } +} diff --git a/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000000 b/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000000 new file mode 100755 index 00000000..51eaa866 --- /dev/null +++ b/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000000 @@ -0,0 +1,1780 @@ +MFEM mesh v1.2 + +# +# MFEM Geometry Types (see mesh/geom.hpp): +# +# POINT = 0 +# SEGMENT = 1 +# TRIANGLE = 2 +# SQUARE = 3 +# TETRAHEDRON = 4 +# CUBE = 5 +# PRISM = 6 +# PYRAMID = 7 +# + +dimension +2 + 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b/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000001 new file mode 100755 index 00000000..c6cce100 --- /dev/null +++ b/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000001 @@ -0,0 +1,1703 @@ +MFEM mesh v1.2 + +# +# MFEM Geometry Types (see mesh/geom.hpp): +# +# POINT = 0 +# SEGMENT = 1 +# TRIANGLE = 2 +# SQUARE = 3 +# TETRAHEDRON = 4 +# CUBE = 5 +# PRISM = 6 +# PYRAMID = 7 +# + +dimension +2 + +elements +282 +1 3 101 84 112 95 +1 3 153 72 173 127 +1 3 115 185 66 138 +1 3 145 137 172 103 +1 3 169 171 32 134 +1 3 106 109 156 87 +1 3 172 43 180 102 +1 3 66 61 65 138 +1 3 41 165 95 112 +1 3 116 154 138 65 +1 3 104 141 139 28 +1 3 35 112 84 33 +1 3 28 133 179 104 +1 3 72 152 186 173 +1 3 184 111 185 115 +1 3 136 137 145 130 +1 3 143 139 141 125 +1 3 64 146 65 62 +1 3 121 129 29 120 +1 3 131 132 2 3 +1 3 65 146 142 116 +1 3 182 107 174 36 +1 3 130 129 126 136 +1 3 51 118 74 49 +1 3 118 51 53 79 +1 3 31 143 125 122 +1 3 151 59 61 66 +1 3 129 121 123 126 +1 3 120 31 122 121 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a/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000015 b/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000015 new file mode 100755 index 00000000..5a23a331 --- /dev/null +++ b/test/issues/data_3960/VisIt_volume/cycle_000000/pmesh.000015 @@ -0,0 +1,1708 @@ +MFEM mesh v1.2 + +# +# MFEM Geometry Types (see mesh/geom.hpp): +# +# POINT = 0 +# SEGMENT = 1 +# TRIANGLE = 2 +# SQUARE = 3 +# TETRAHEDRON = 4 +# CUBE = 5 +# PRISM = 6 +# PYRAMID = 7 +# + +dimension +2 + +elements +279 +1 3 3 4 38 36 +1 3 37 38 4 5 +1 3 6 0 7 39 +1 3 5 6 39 37 +2 3 95 52 124 94 +2 3 126 81 123 102 +2 3 90 118 50 105 +2 3 59 111 124 109 +2 3 43 8 9 88 +2 3 110 93 113 42 +2 3 100 41 114 83 +2 3 103 82 119 49 +2 3 79 89 50 118 +2 3 84 64 117 85 +2 3 89 22 23 50 +2 3 62 63 99 55 +2 3 62 67 68 63 +2 3 92 45 47 48 +2 3 68 71 72 70 +2 3 22 89 41 21 +2 3 92 48 55 99 +2 3 24 105 50 23 +2 3 55 48 47 54 +2 3 98 75 74 73 +2 3 44 46 47 45 +2 3 96 78 86 87 +2 3 97 5 4 64 +2 3 45 0 6 44 +2 3 80 94 66 61 +2 3 77 76 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mfem.MakeParFilename(testDataFolder+'/VisIt_volume/cycle_000000/pmesh.', myid) +pmesh = mfem.ParMesh(MPI.COMM_WORLD, fname) + +### loading of the pressure field from the VisIt data collection +visit_dc = mfem.VisItDataCollection(testDataFolder+'/VisIt_volume/cycle') +visit_dc.SetMesh(MPI.COMM_WORLD, pmesh) +visit_dc.Load(0) +p = visit_dc.GetParField("pressure") + +p.Save('ppressure.'+smyid) +pmesh.Print('pmesh.'+smyid) + +smesh = pmesh.GetSerialMesh(0) +sp = p.GetSerialGridFunction(0, smesh); + +if myid == 0: + sp.Save('spressure') + smesh.Print('smesh') + +### printing additional information on the mesh +mesh_mfem = visit_dc.GetMesh() +mesh_data = mesh_mfem.GetNodes() # .GetTrueVector() +order = int(mesh_mfem.GetNodalFESpace().FEColl().GetOrder()) +dim = mesh_mfem.GetNodes().VectorDim() +dof = int(mesh_data.Size()/dim) # scalar degree of freedom, to be multiplied by number of scalar variables to have total dof +nele = mesh_mfem.GetNE() # .GetGlobalNE() +mesh_point_ordering = mesh_mfem.GetNodes().FESpace().GetOrdering() # "Ordering::byNODES=0" or "Ordering::byVDIM=1" + +if myid == 0: + print("dim="+str(dim)) + print("numb elem="+str(nele)) + print("order="+str(order)) + print("scalar dof="+str(int(dof))) + print("pmesh_point_ordering ="+str(mesh_point_ordering)) + +### save the mesh in serial format +if myid == 0: + folderList = [testDataFolder+'/VisIt_volume_serial/'] + for folderName in folderList: + if not os.path.exists(folderName): + os.mkdir(folderName) + +if myid == 0: + visit_dc_out = mfem.VisItDataCollection(testDataFolder+'/VisIt_volume_serial/cycle', smesh) + visit_dc_out.SetLevelsOfDetail(order) + visit_dc_out.RegisterField("pressure", sp) + visit_dc_out.SetCycle(0) + visit_dc_out.SetTime(0) + visit_dc_out.SetFormat(mfem.DataCollection.SERIAL_FORMAT) + visit_dc_out.Save() diff --git a/test/test_array2.py b/test/test_array2.py new file mode 100644 index 00000000..e2d92b78 --- /dev/null +++ b/test/test_array2.py @@ -0,0 +1,37 @@ +from __future__ import print_function +import os +import sys +import numpy as np + +if len(sys.argv) > 1 and sys.argv[1] == '-p': + import mfem.par as mfem + use_parallel = True + from mfem.common.mpi_debug import nicePrint as print + from mpi4py import MPI + myid = MPI.COMM_WORLD.rank + +else: + import mfem.ser as mfem + use_parallel = False + myid = 0 + +def run_test(): + a = mfem.uintArray(5) + b = mfem.int8Array(5) + c = mfem.int64Array(5) + d = mfem.boolArray(5) + + def check(a, value): + a.GetDataArray()[:] = value + print(a[0], a[-1], type(a[0]), ) + assert a[0] == value, "Array data element does not agree" + + + check(a, 5) + check(b, 100) + check(c, 1000) + check(d, True) + + +if __name__=='__main__': + run_test()